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Vacher JP, Kok PJR, Rodrigues MT, Lima A, Hrbek T, Werneck FP, Manzi S, Thébaud C, Fouquet A. Diversification of the terrestrial frog genus Anomaloglossus (Anura, Aromobatidae) in the Guiana Shield proceeded from highlands to lowlands, with successive loss and reacquisition of endotrophy. Mol Phylogenet Evol 2024; 192:108008. [PMID: 38181828 DOI: 10.1016/j.ympev.2023.108008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 09/23/2023] [Accepted: 12/30/2023] [Indexed: 01/07/2024]
Abstract
Two main landscapes emerge from the Guiana Shield: the highlands to the west called the Pantepui region and the Amazonian lowlands to the east, both harbouring numerous endemic species. With 32 currently recognized species, the genus Anomaloglossus stands out among Neotropical frogs as one that diversified only within the Guiana Shield both in the highlands and the lowlands. We present a time-calibrated phylogeny obtained by using combined mitogenomic and nuclear DNA, which suggests that the genus originates from Pantepui where extant lineages started diversifying around 21 Ma, and subsequently (ca. 17 Ma) dispersed during the Miocene Climatic Optimum to the lowlands of the eastern Guiana Shield where the ability to produce endotrophic tadpoles evolved. Further diversification within the lowlands in the A. stepheni group notably led to an evolutionary reversal toward exotrophy in one species group during the late Miocene, followed by reacquisition of endotrophy during the Pleistocene. These successive shifts of reproductive mode seem to have accompanied climatic oscillations. Long dry periods might have triggered evolution of exotrophy, whereas wetter climates favoured endotrophic forms, enabling colonization of terrestrial habitats distant from water. Acquisition, loss, and reacquisition of endotrophy makes Anomaloglossus unique among frogs and may largely explain the current species diversity. The micro evolutionary processes involved in these rapid shifts of reproductive mode remain to be revealed.
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Affiliation(s)
- Jean-Pierre Vacher
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300 CNRS-IRD-TINP-UPS3, Université Paul Sabatier, Toulouse, France.
| | - Philippe J R Kok
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Łódź, 12/16 Banacha Str, Łódź 90-237, Poland; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
| | - Miguel Trefaut Rodrigues
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, Caixa Postal 11.461, CEP 05508-090 São Paulo, Brazil
| | - Albertina Lima
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Avenida André Araújo 2936, 69080-971 Manaus, AM, Brazil
| | - Tomas Hrbek
- Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, 69080-900 Manaus, AM, Brazil
| | - Fernanda P Werneck
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Avenida André Araújo 2936, 69080-971 Manaus, AM, Brazil
| | - Sophie Manzi
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300 CNRS-IRD-TINP-UPS3, Université Paul Sabatier, Toulouse, France
| | - Christophe Thébaud
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300 CNRS-IRD-TINP-UPS3, Université Paul Sabatier, Toulouse, France
| | - Antoine Fouquet
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300 CNRS-IRD-TINP-UPS3, Université Paul Sabatier, Toulouse, France
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2
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Kuderna LFK, Ulirsch JC, Rashid S, Ameen M, Sundaram L, Hickey G, Cox AJ, Gao H, Kumar A, Aguet F, Christmas MJ, Clawson H, Haeussler M, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J, Rouselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, Schraiber JG, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Valsecchi J, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin AD, Guschanski K, Schierup MH, Beck RMD, Karakikes I, Wang KC, Umapathy G, Roos C, Boubli JP, Siepel A, Kundaje A, Paten B, Lindblad-Toh K, Rogers J, Marques Bonet T, Farh KKH. Identification of constrained sequence elements across 239 primate genomes. Nature 2024; 625:735-742. [PMID: 38030727 PMCID: PMC10808062 DOI: 10.1038/s41586-023-06798-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023]
Abstract
Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3-9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.
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Affiliation(s)
- Lukas F K Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Jacob C Ulirsch
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Sabrina Rashid
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Mohamed Ameen
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Laksshman Sundaram
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Glenn Hickey
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Anthony J Cox
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Arvind Kumar
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Francois Aguet
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Matthew J Christmas
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Hiram Clawson
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | | | - Mareike C Janiak
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Martin Kuhlwilm
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Joseph D Orkin
- Département d'Anthropologie, Université de Montréal, Montréal, Quebec, Canada
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Alejandro Valenzuela
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Tefé, Brazil
- Evolutionary Biology and Ecology (EBE), Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Lidia Agueda
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Julie Blanc
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Marta Gut
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Ian Goodhead
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
| | | | - Julie E Horvath
- North Carolina Museum of Natural Sciences, Raleigh, NC, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - David Juan
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | | | - Fabrício Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City, UT, USA
| | | | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Brazil
| | - João Valsecchi
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Brazil
- Rede de Pesquisa em Diversidade, Conservação e Uso da Fauna da Amazônia - RedeFauna, Manaus, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica-ComFauna, Iquitos, Peru
| | - Malu Messias
- Universidade Federal de Rondônia, Porto Velho, Brazil
| | | | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Rogerio Rossi
- Instituto de Biociências, Universidade Federal do Mato Grosso, Cuiabá, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Brazil
- Department of Biology, Trinity University, San Antonio, TX, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clément J Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clifford J Jolly
- Department of Anthropology, New York University, New York, NY, USA
| | - Jane Phillips-Conroy
- Department of Neuroscience, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop, TX, USA
| | - Christian Abee
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop, TX, USA
| | - Joe H Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop, TX, USA
| | | | - Sree Kanthaswamy
- School of Interdisciplinary Forensics, Arizona State University, Phoenix, AZ, USA
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Fekadu Shiferaw
- Guinea Worm Eradication Program, The Carter Center Ethiopia, Addis Ababa, Ethiopia
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Long Zhou
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
- Professorship for International Animal Health/One Health, Faculty of Veterinary Medicine, Justus Liebig University, Giessen, Germany
| | - Minh D Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
| | - Esther Lizano
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | - Arcadi Navarro
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Barcelonaβeta Brain Research Center, Pasqual Maragall Foundation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | | | - Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK
- School of Geosciences, Edinburgh, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, Göttingen, Germany
| | - Ivo Gut
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Robin M D Beck
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Ioannis Karakikes
- Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Kevin C Wang
- Department of Cancer Biology, Stanford University, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Jean P Boubli
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Tomas Marques Bonet
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain.
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA.
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3
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Banhos A, Sanaiotti TM, Coser R, Gravena W, Aguiar-Silva FH, Kaizer M, Hrbek T, Farias IP. Long-term female bias in sex ratios across life stages of Harpy Eagle, a large raptor exhibiting reverse sexual size dimorphism. R Soc Open Sci 2023; 10:231443. [PMID: 38026037 PMCID: PMC10645098 DOI: 10.1098/rsos.231443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023]
Abstract
The primary (PSR), secondary (SSR) and adult (ASR) sex ratios of sexually reproducing organisms influence their life histories. Species exhibiting reversed sexual size dimorphism (RSD) may imply a higher cost of female production or lower female survival, thus generating biases in PSR, SSR and/or ASR towards males. The Harpy Eagle is the world's largest eagle exhibiting RSD. This species is found in the Neotropical region and is currently threatened with extinction. We used molecular markers to determine the sex of 309 Harpy Eagles spanning different life stages-eaglets, subadults and adults-from 1904 to 2021 within the Amazon Rainforest and Atlantic Forest. Sex ratios for all life stages revealed a female-biased deviation across all periods and regions. Our results suggest that the population bias towards females is an evolutionary ecological pattern of this species, and SSR and ASR likely emerged from the PSR. This natural bias towards females may be compensated by an earlier sexual maturation age of males, implying a longer reproductive lifespan and a higher proportion of sexually active males. A better understanding of the Harpy Eagle's life history can contribute to understanding sex-role evolution and enable more appropriate conservation strategies for the species.
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Affiliation(s)
- Aureo Banhos
- Departamento de Biologia, Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo - UFES, Alto Universitário, s/n°, Guararema, 29500-000 Alegre, Espírito Santo, Brazil
- Programa de Pós-Graduação em Ciências Biológicas (Biologia Animal) - PPGBAN, Universidade Federal do Espírito Santo - UFES, Avenida Fernando Ferrari, 514, Prédio Barbara Weinberg, 29075-910 Vitória, Espírito Santo, Brazil
- Projeto Harpia (Harpy Eagle Project - Brazil), Instituto Nacional de Pesquisas da Amazônia – INPA, Av. André Araújo, 2936, Aleixo, 69067-375 Manaus, Amazonas, Brazil
- Projeto Harpia – Mata Atlântica (Harpy Eagle Project - Atlantic Forest), Universidade Federal do Espírito Santo - UFES, Alto Universitário, Guararema, 29500-000 Alegre, Espírito Santo, Brazil
- Laboratório de Evolução e Genética Animal - LEGAL, Universidade Federal do Amazonas - UFAM, Av. General Rodrigo Octavio Jordão Ramos, 6200 - Coroado I, 69080-900 Manaus, Amazonas, Brazil
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia - INPA, Av. André Araújo, 2936, Aleixo, 69067-375 Manaus, Amazonas, Brazil
| | - Tânia Margarete Sanaiotti
- Projeto Harpia (Harpy Eagle Project - Brazil), Instituto Nacional de Pesquisas da Amazônia – INPA, Av. André Araújo, 2936, Aleixo, 69067-375 Manaus, Amazonas, Brazil
- Projeto Harpia – Mata Atlântica (Harpy Eagle Project - Atlantic Forest), Universidade Federal do Espírito Santo - UFES, Alto Universitário, Guararema, 29500-000 Alegre, Espírito Santo, Brazil
- Coordenaçãode Biodiversidade, Instituto Nacional de Pesquisas da Amazônia - INPA, Av. André Araújo, 2936, Aleixo, 69067-375 Manaus, Amazonas, Brazil
| | - Renan Coser
- Projeto Harpia (Harpy Eagle Project - Brazil), Instituto Nacional de Pesquisas da Amazônia – INPA, Av. André Araújo, 2936, Aleixo, 69067-375 Manaus, Amazonas, Brazil
- Projeto Harpia – Mata Atlântica (Harpy Eagle Project - Atlantic Forest), Universidade Federal do Espírito Santo - UFES, Alto Universitário, Guararema, 29500-000 Alegre, Espírito Santo, Brazil
- Laboratório de Evolução e Genética Animal - LEGAL, Universidade Federal do Amazonas - UFAM, Av. General Rodrigo Octavio Jordão Ramos, 6200 - Coroado I, 69080-900 Manaus, Amazonas, Brazil
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia - INPA, Av. André Araújo, 2936, Aleixo, 69067-375 Manaus, Amazonas, Brazil
| | - Waleska Gravena
- Laboratório de Evolução e Genética Animal - LEGAL, Universidade Federal do Amazonas - UFAM, Av. General Rodrigo Octavio Jordão Ramos, 6200 - Coroado I, 69080-900 Manaus, Amazonas, Brazil
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia - INPA, Av. André Araújo, 2936, Aleixo, 69067-375 Manaus, Amazonas, Brazil
- Instituto de Saúde e Biotecnologia, Universidade Federal do Amazonas - UFAM, Estrada Coari Mamiá, 305, Espírito Santo, 69460-000 Coari, Amazonas, Brazil
| | - Francisca Helena Aguiar-Silva
- Projeto Harpia (Harpy Eagle Project - Brazil), Instituto Nacional de Pesquisas da Amazônia – INPA, Av. André Araújo, 2936, Aleixo, 69067-375 Manaus, Amazonas, Brazil
- Projeto Harpia – Mata Atlântica (Harpy Eagle Project - Atlantic Forest), Universidade Federal do Espírito Santo - UFES, Alto Universitário, Guararema, 29500-000 Alegre, Espírito Santo, Brazil
- Coordenaçãode Biodiversidade, Instituto Nacional de Pesquisas da Amazônia - INPA, Av. André Araújo, 2936, Aleixo, 69067-375 Manaus, Amazonas, Brazil
| | - Mylena Kaizer
- Projeto Harpia (Harpy Eagle Project - Brazil), Instituto Nacional de Pesquisas da Amazônia – INPA, Av. André Araújo, 2936, Aleixo, 69067-375 Manaus, Amazonas, Brazil
- Projeto Harpia – Mata Atlântica (Harpy Eagle Project - Atlantic Forest), Universidade Federal do Espírito Santo - UFES, Alto Universitário, Guararema, 29500-000 Alegre, Espírito Santo, Brazil
- Laboratório de Evolução e Genética Animal - LEGAL, Universidade Federal do Amazonas - UFAM, Av. General Rodrigo Octavio Jordão Ramos, 6200 - Coroado I, 69080-900 Manaus, Amazonas, Brazil
- Programa de Pós-Graduação em Zoologia - PPGZOO, Universidade Federal do Amazonas - UFAM, Av. General Rodrigo Octavio Jordão Ramos, 6200, Coroado I, 69080-900 Manaus, Amazonas, Brazil
| | - Tomas Hrbek
- Projeto Harpia (Harpy Eagle Project - Brazil), Instituto Nacional de Pesquisas da Amazônia – INPA, Av. André Araújo, 2936, Aleixo, 69067-375 Manaus, Amazonas, Brazil
- Laboratório de Evolução e Genética Animal - LEGAL, Universidade Federal do Amazonas - UFAM, Av. General Rodrigo Octavio Jordão Ramos, 6200 - Coroado I, 69080-900 Manaus, Amazonas, Brazil
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia - INPA, Av. André Araújo, 2936, Aleixo, 69067-375 Manaus, Amazonas, Brazil
- Programa de Pós-Graduação em Zoologia - PPGZOO, Universidade Federal do Amazonas - UFAM, Av. General Rodrigo Octavio Jordão Ramos, 6200, Coroado I, 69080-900 Manaus, Amazonas, Brazil
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas - UFAM, Av. General Rodrigo Octavio Jordão Ramos, 6200, Coroado I, 69080-900 Manaus, Amazonas, Brazil
- Department of Biology, Trinity University, San Antonio, TX 78212, USA
| | - Izeni Pires Farias
- Projeto Harpia (Harpy Eagle Project - Brazil), Instituto Nacional de Pesquisas da Amazônia – INPA, Av. André Araújo, 2936, Aleixo, 69067-375 Manaus, Amazonas, Brazil
- Laboratório de Evolução e Genética Animal - LEGAL, Universidade Federal do Amazonas - UFAM, Av. General Rodrigo Octavio Jordão Ramos, 6200 - Coroado I, 69080-900 Manaus, Amazonas, Brazil
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia - INPA, Av. André Araújo, 2936, Aleixo, 69067-375 Manaus, Amazonas, Brazil
- Programa de Pós-Graduação em Zoologia - PPGZOO, Universidade Federal do Amazonas - UFAM, Av. General Rodrigo Octavio Jordão Ramos, 6200, Coroado I, 69080-900 Manaus, Amazonas, Brazil
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas - UFAM, Av. General Rodrigo Octavio Jordão Ramos, 6200, Coroado I, 69080-900 Manaus, Amazonas, Brazil
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4
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Costa-Araújo R, Bergamasco G, Roos C, Farias IP, Hrbek T. Notes on the distribution and habitat use of marmosets (Callitrichidae: Mico) from south-central Amazonia. Primate Biol 2023; 10:7-11. [PMID: 37560614 PMCID: PMC10407307 DOI: 10.5194/pb-10-7-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 06/13/2023] [Indexed: 08/11/2023] Open
Abstract
Currently, 15 species of Amazon marmosets (genus Mico) are known to science. The Amazon marmosets occur primarily in southern Brazilian Amazonia, the arc of deforestation, and are among the least studied primates of the neotropics. This is particularly the case for M. acariensis and M. chrysoleucos, both endemic to the Aripuanã-Sucundurí interfluve, south-central Amazonia. Mico acariensis was not studied beyond the species description, and the only information currently available is the pelage colouration of the holotype, inferred coordinates of the type locality, and a field report with two additional localities of occurrence. Regarding M. chrysoleucos, in addition to the species description, there are taxonomic reviews, the report of a second occurrence record, and a study on the species range. We provide here new occurrence records that extend the distribution of M. chrysoleucos; provide new records for and update the distribution of M. acariensis; and propose the existence of a hybrid zone in the Aripuanã-Sucundurí interfluve, i.e. around the known distribution boundaries of M. acariensis, M. chrysoleucos, and M. melanurus, and we also discuss habitat use patterns of Amazon marmosets.
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Affiliation(s)
- Rodrigo Costa-Araújo
- Primates Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Giovanna Bergamasco
- Graduate Program in Ecology, Evolution and Biodiversity, São Paulo State University, Rio Claro, 13506-900, Brazil
| | - Christian Roos
- Primates Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Izeni Pires Farias
- Evolution and Animal Genetics Laboratory, Federal University of Amazonas, Manaus, 69077-000, Brazil
| | - Tomas Hrbek
- Evolution and Animal Genetics Laboratory, Federal University of Amazonas, Manaus, 69077-000, Brazil
- Department of Biology, Trinity University, San Antonio, Texas 78212-7200, United States of America
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5
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Carneiro J, Sampaio I, Silva-Júnior JDSE, Martins-Junior A, Farias I, Hrbek T, Boubli J, Schneider H. Molecular Evidence Supports Five Lineages within Chiropotes (Pitheciidae, Platyrrhini). Genes (Basel) 2023; 14:1309. [PMID: 37510215 PMCID: PMC10379672 DOI: 10.3390/genes14071309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 07/30/2023] Open
Abstract
Pitheciines have unique dental specializations among New World monkeys that allow them to feed on fruits with hard pericarps, thus playing a major role as seed predators. The three extant pitheciine genera, Pithecia, Cacajao and Chiropotes, are all endemic to the Amazon region. Because of the uncertainties about interspecific relationships, we reviewed the systematics and taxonomy of the genus Chiropotes. The phylogenetic analyses were performed based on Maximum Likelihood and Bayesian Inference, while species delimitation analyses were carried out using multispecies coalescent methods. In addition, we estimated genetic distances, divergence time and the probable ancestral distribution of this genus. Our results support five species of Chiropotes that emerged during the Plio-Pleistocene. Biogeographic estimates suggest that the ancestor of the current Chiropotes species occupied the endemism areas from Rondônia and Tapajós. Later, subsequent radiation and founder effects associated with the formation of the Amazonian basins probably determined the speciation events within Chiropotes.
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Affiliation(s)
- Jeferson Carneiro
- Institute of Coastal Studies, University Campus of Bragança, Federal University of Pará, Belém 66075-110, Pará, Brazil
| | - Iracilda Sampaio
- Institute of Coastal Studies, University Campus of Bragança, Federal University of Pará, Belém 66075-110, Pará, Brazil
| | | | - Antonio Martins-Junior
- Federal Institute of Education, Science and Technology of Pará, Campus Tucuruí, Tucuruí 68455-210, Pará, Brazil
| | - Izeni Farias
- Laboratório de Evolução e Genética Animal, Federal University of Amazonas, Manaus 69067-005, Amazonas, Brazil
| | - Tomas Hrbek
- Laboratório de Evolução e Genética Animal, Federal University of Amazonas, Manaus 69067-005, Amazonas, Brazil
| | - Jean Boubli
- School of Environment and Life Sciences, University of Salford, Salford M5 4WT, UK
| | - Horacio Schneider
- Institute of Coastal Studies, University Campus of Bragança, Federal University of Pará, Belém 66075-110, Pará, Brazil
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6
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Nunes I, Passos K, Mourão Ximenes A, Hrbek T, Farias IP. Spatial and temporal population genetic analysis of Semaprochilodus insignis (Prochilodontidae), an overexploited fish from the Amazon basin. PeerJ 2023; 11:e15503. [PMID: 37361032 PMCID: PMC10289084 DOI: 10.7717/peerj.15503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 05/14/2023] [Indexed: 06/28/2023] Open
Abstract
Background Semaprochilodus insignis is a migratory fish of commercial and subsistence importance to communities in the Amazon. Despite the high intensity of exploitation, recent studies have not been carried out to assess the genetic status of its stocks. Methods This study is the first to estimate genetic diversity and to test the existence of spatial and temporal structuring of S. insignis through sequencing of the mtDNA control region (n = 241) and eight microsatellite loci (n = 180) of individuals sampled at 11 sites distributed in the Brazilian Amazon basin. Results Results for both markers were congruent, revealing a homogeneous genetic diversity in all the sampled locations, in addition to the absence of spatial and temporal genetic structure, indicating that the species forms a large panmictic population in the Brazilian Amazon. Discussion Although overfishing does not yet appear to have affected the levels of genetic variability of S. insignis, signals of reduction of the effective population size and a bottleneck provide an early alert to the effects of overfishing. Thus, the ever-decreasing populations may threaten S. insignis in the future. Therefore, it is hoped that the results of this study may contribute to the elaboration of management plans or any other measures that aim at the management and conservation of this species of great importance for the Amazon basin.
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Affiliation(s)
- Ingrid Nunes
- Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Universidade Federal do Amazonas, Manaus, Amazonas, Brasil
| | - Kelmer Passos
- Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Universidade Federal do Amazonas, Manaus, Amazonas, Brasil
| | - Aline Mourão Ximenes
- Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Universidade Federal do Amazonas, Manaus, Amazonas, Brasil
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brasil
| | - Tomas Hrbek
- Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Universidade Federal do Amazonas, Manaus, Amazonas, Brasil
- Department of Biology, Trinity University, San Antonio, TX, United States of America
| | - Izeni Pires Farias
- Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Universidade Federal do Amazonas, Manaus, Amazonas, Brasil
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7
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Sanchez-Bernal D, Martinez JG, Farias IP, Hrbek T, Caballero S. Phylogeography and population genetic structure of the cardinal tetra ( Paracheirodon axelrodi) in the Orinoco basin and Negro River (Amazon basin): evaluating connectivity and historical patterns of diversification. PeerJ 2023; 11:e15117. [PMID: 37309369 PMCID: PMC10257900 DOI: 10.7717/peerj.15117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 03/02/2023] [Indexed: 06/14/2023] Open
Abstract
The Neotropics contain one of the most diverse assemblages of freshwater fishes worldwide. Part of this diversity is shared between the Orinoco and Amazon basins. These basins have been separated for a long time due to the Vaupes Arch, rising between 10-11 Ma. Today, there is only one permanent connection between the Orinoco and Negro (Amazon) basins, known as the Casiquiare Canal. However, alternative corridors allowing fish dispersion between both basins have been proposed. The cardinal tetra (Paracheirodon axelrodi), the most important fish in the ornamental world market, is distributed in both basins. Here we investigated P. axelrodi phylogeography, population structure, and potential routes of migration and connectivity between the two basins. A total of 468 bp of the mitochondrial gene (COI), 555 bp of the nuclear gene fragment (MYH6), and eight microsatellite loci were analyzed. As a result, we found two major genetic clusters as the most likely scenario (K = 2), but they were not discreetly distributed between basins. A gradient of genetic admixture was observed in Cucui and São Gabriel da Cachoeira, between the upper Negro River and the upper Orinoco. Samples from the middle-lower Negro River were highly structured. Cucui (Negro basin) was more similar to the Orinoco than to the rest of the Negro basin populations. However, substructure was also observed by the discriminant analysis, fixation indices and other hierarchichal structure analyses (K = 3 - 6), showing three major geographic clusters: Orinoco, Cucui, and the remaining Negro basin. Unidirectional migration patterns were detected between basins: via Cucui toward Orinoco and via the remaining of the Negro basin toward Orinoco. Results from the Relaxed Random Walk analysis support a very recent origin of this species in the headwater Orinoco basin (Western Guiana Shield, at late Pleistocene) with a later rapid colonization of the remaining Orinoco basin and almost simultaneously the Negro River via Cucui, between 0.115 until about 0.001 Ma. Historical biogeography and population genetic patterns observed here for Cardinal tetra, seem to be better explained by river capture, physical, or ecological barriers than due to the geographic distance.
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Affiliation(s)
| | - José Gregorio Martinez
- Grupo de Investigación Biociencias, Facultad de Ciencias de la Salud, Institución Universitaria Colegio Mayor de Antioquia, Medellín, Antioquia, Colombia
| | | | - Tomas Hrbek
- Departamento de Genética, Universidade do Amazonas, Manaos, Brazil
| | - Susana Caballero
- Biological Sciences Department, Universidad de Los Andes, Bogota, Colombia
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8
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Kuderna LFK, Gao H, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, Schraiber JG, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Valsecchi J, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin AD, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Rogers J, Farh KKH, Marques Bonet T. A global catalog of whole-genome diversity from 233 primate species. Science 2023; 380:906-913. [PMID: 37262161 DOI: 10.1126/science.abn7829] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/06/2023] [Indexed: 06/03/2023]
Abstract
The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.
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Affiliation(s)
- Lukas F K Kuderna
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Mareike C Janiak
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Martin Kuhlwilm
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Austria
| | - Joseph D Orkin
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Département d'anthropologie, Université de Montréal, 3150 Jean-Brillant, Montréal, QC H3T 1N8, Canada
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Alejandro Valenzuela
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Estrada da Bexiga 2584, CEP 69553-225, Tefé, Amazonas, Brazil
- Evolutionary Biology and Ecology (EBE), Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Av. Franklin D. Roosevelt 50, CP 160/12, B-1050 Brussels Belgium
| | - Lidia Agueda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
| | | | - Julie E Horvath
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC 27707, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
| | | | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | | | - Fabrício Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City. UT 84102, USA
| | | | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
| | - João Valsecchi
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Amazonas, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia - RedeFauna, Manaus, Amazonas, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica - ComFauna, Iquitos, Loreto, Peru
| | - Malu Messias
- Universidade Federal de Rondônia, Porto Velho, Rondônia, Brazil
| | | | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Rogerio Rossi
- Instituto de Biociências, Universidade Federal do Mato Grosso, Cuiabá, MT, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
- Department of Biology, Trinity University, San Antonio, TX 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clément J Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clifford J Jolly
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Jane Phillips-Conroy
- Department of Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | - Christian Abee
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | - Joe H Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | | | - Sree Kanthaswamy
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ 85004, USA
| | - Fekadu Shiferaw
- Guinea Worm Eradication Program, The Carter Center Ethiopia, Addis Ababa, Ethiopia
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Long Zhou
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Guojie Zhang
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
- Women's Hospital, School of Medicine, Zhejiang University, 1 Xueshi Road, Shangcheng District, Hangzhou 310006, China
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Head Office, P.O. Box 661, Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany
| | - Minh D Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
| | - Esther Lizano
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | - Arcadi Navarro
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra. Pg. Luís Companys 23, 08010 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Av. Doctor Aiguader, N88, 08003 Barcelona, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, C. Wellington 30, 08005 Barcelona, Spain
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Ninh Binh Province, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Jessica Lee
- Mandai Nature, 80 Mandai Lake Road, Singapore
| | - Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK, and School of Geosciences, Drummond Street, Edinburgh EH8 9XP, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37077 Göttingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
- Department of Medical Genetics, University of Calgary, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Jean P Boubli
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Tomas Marques Bonet
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra. Pg. Luís Companys 23, 08010 Barcelona, Spain
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9
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Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich ASD, Fiziev PP, Kuderna LFK, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, do Amaral JV, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Bataillon T, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin A, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Lek M, Sunyaev S, O'Donnell-Luria A, Rehm HL, Xu J, Rogers J, Marques-Bonet T, Farh KKH. The landscape of tolerated genetic variation in humans and primates. Science 2023; 380:eabn8153. [PMID: 37262156 DOI: 10.1126/science.abn8197] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/22/2023] [Indexed: 06/03/2023]
Abstract
Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.
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Affiliation(s)
- Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Tobias Hamp
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Jeffrey Ede
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Jeremy McRae
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
| | - Yanshen Yang
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | | | - Petko P Fiziev
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Lukas F K Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Laksshman Sundaram
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Yibing Wu
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Aashish Adhikari
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Yair Field
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Chen Chen
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Serafim Batzoglou
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Francois Aguet
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Rebecca Reimers
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Daniel Balick
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Mareike C Janiak
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030 Vienna, Austria
| | - Joseph D Orkin
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Département d'anthropologie, Université de Montréal, 3150 Jean-Brillant, Montréal, QC H3T 1N8, Canada
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Alejandro Valenzuela
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University, 8000 Aarhus, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Estrada da Bexiga 2584, Tefé, Amazonas, CEP 69553-225, Brazil
- Evolutionary Biology and Ecology (EBE), Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Av. Franklin D. Roosevelt 50, CP 160/12, B-1050 Brussels, Belgium
| | - Lidia Agueda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
| | | | - Julie E Horvath
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC 27707, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | | | - Fabrício Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas, 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City, UT 84102, USA
| | - Iracilda Sampaio
- Universidade Federal do Para, Guamá, Belém - PA, 66075-110, Brazil
| | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas, 69080-900, Brazil
| | - João Valsecchi do Amaral
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Amazonas, 69553-225, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia - RedeFauna, Manaus, Amazonas, 69080-900, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica - ComFauna, Iquitos, Loreto, 16001, Peru
| | - Mariluce Messias
- Universidade Federal de Rondonia, Porto Velho, Rondônia, 78900-000, Brazil
- PPGREN - Programa de Pós-Graduação "Conservação e Uso dos Recursos Naturais and BIONORTE - Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Rede BIONORTE, Universidade Federal de Rondonia, Porto Velho, Rondônia, 78900-000, Brazil
| | - Maria N F da Silva
- Instituto Nacional de Pesquisas da Amazonia, Petrópolis, Manaus - AM, 69067-375, Brazil
| | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Rogerio Rossi
- Universidade Federal do Mato Grosso, Boa Esperança, Cuiabá - MT, 78060-900, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas, 69080-900, Brazil
- Department of Biology, Trinity University, San Antonio, TX 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, 401, Madagascar
| | - Clément J Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, 401, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, 401, Madagascar
| | | | | | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christian Abee
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Joe H Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Eduardo Fernandez-Duque
- Yale University, New Haven, CT 06520, USA
- Universidad Nacional de Formosa, Argentina Fundacion ECO, Formosa, Argentina
| | | | - Fekadu Shiferaw
- Guinea Worm Eradication Program, The Carter Center Ethiopia, PoB 16316, Addis Ababa 1000, Ethiopia
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Long Zhou
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
- Women's Hospital, School of Medicine, Zhejiang University, 1 Xueshi Road, Shangcheng District, Hangzhou 310006, China
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Head Office, P.O. Box 661, Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald - Insei Riems, Germany
| | - Minh D Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi 100000, Vietnam
| | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, 70191 Stuttgart, Germany
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Av. Doctor Aiguader, N88, 08003 Barcelona, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, C. Wellington 30, 08005 Barcelona, Spain
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Ninh Binh Province 430000, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Jessica Lee
- Mandai Nature, 80 Mandai Lake Road, Singapore 729826, Republic of Singapore
| | - Patrick Tan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore 168582, Republic of Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore 168582, Republic of Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore 168582, Republic of Singapore
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK
- School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH8 9XP, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz Science Campus Primate Cognition, 37077 Göttingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra, Pg. Luís Companys 23, 08010 Barcelona, Spain
| | - Amanda Melin
- Department of Anthropology & Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
- Department of Medical Genetics, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH8 9XP, UK
| | | | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Jean P Boubli
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Shamil Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jinbo Xu
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
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10
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Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich A, Fiziev P, Kuderna L, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rouselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath J, Hvilsom C, Juan D, Frandsen P, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, do Amaral JV, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Batallion T, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin A, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Lek M, Sunyaev S, O’Donnell A, Rehm H, Xu J, Rogers J, Marques-Bonet T, Kai-How Farh K. The landscape of tolerated genetic variation in humans and primates. bioRxiv 2023:2023.05.01.538953. [PMID: 37205491 PMCID: PMC10187174 DOI: 10.1101/2023.05.01.538953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these variants can be inferred to have non-deleterious effects in human based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases. One Sentence Summary Deep learning classifier trained on 4.3 million common primate missense variants predicts variant pathogenicity in humans.
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Affiliation(s)
- Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Tobias Hamp
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Jeffrey Ede
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Joshua G. Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Jeremy McRae
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
| | - Yanshen Yang
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Anastasia Dietrich
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Petko Fiziev
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Lukas Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Laksshman Sundaram
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Yibing Wu
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Aashish Adhikari
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Yair Field
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Chen Chen
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Serafim Batzoglou
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Francois Aguet
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Rebecca Reimers
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Daniel Balick
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Mareike C. Janiak
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna; Djerassiplatz 1, 1030, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna; 1030, Vienna, Austria
| | - Joseph D. Orkin
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Département d’anthropologie, Université de Montréal; 3150 Jean-Brillant, Montréal, QC, H3T 1N8, Canada
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR); Ghaziabad, 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology; Hyderabad, 500007, India
| | - Alejandro Valenzuela
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University; Aarhus, 8000, Denmark
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University; Aarhus, 8000, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development; Estrada da Bexiga 2584, Tefé, Amazonas, CEP 69553-225, Brazil
- Faculty of Sciences, Department of Organismal Biology, Unit of Evolutionary Biology and Ecology, Université Libre de Bruxelles (ULB); Avenue Franklin D. Roosevelt 50, 1050, Brussels, Belgium
| | - Lidia Agueda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, Texas, 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, Texas, 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University; SE-75236, Uppsala, Sweden
| | | | - Julie Horvath
- North Carolina Museum of Natural Sciences; Raleigh, North Carolina, 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University; Durham, North Carolina , 27707, USA
- Department of Biological Sciences, North Carolina State University; Raleigh, North Carolina , 27695, USA
- Department of Evolutionary Anthropology, Duke University; Durham, North Carolina , 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | | | - Fabricio Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL); Manaus, Amazonas, 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah; Salt Lake City, Utah, 84102, USA
| | - Iracilda Sampaio
- Universidade Federal do Para; Guamá, Belém - PA, 66075-110, Brazil
| | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL); Manaus, Amazonas, 69080-900, Brazil
| | - João Valsecchi do Amaral
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development; Tefé, Amazonas, 69553-225, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia – RedeFauna; Manaus, Amazonas, 69080-900, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica – ComFauna; Iquitos, Loreto, 16001, Peru
| | - Mariluce Messias
- Universidade Federal de Rondonia; Porto Velho, Rondônia, 78900-000, Brazil
- PPGREN - Programa de Pós-Graduação “Conservação e Uso dos Recursos Naturais and BIONORTE - Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Rede BIONORTE, Universidade Federal de Rondonia; Porto Velho, Rondônia, 78900-000, Brazil
| | - Maria N. F. da Silva
- Instituto Nacional de Pesquisas da Amazonia; Petrópolis, Manaus - AM, 69067-375, Brazil
| | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology; Hyderabad, 500007, India
| | - Rogerio Rossi
- Universidade Federal do Mato Grosso; Boa Esperança, Cuiabá - MT, 78060-900, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL); Manaus, Amazonas, 69080-900, Brazil
- Department of Biology, Trinity University; San Antonio, Texas, 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga; Mahajanga, 401, Madagascar
| | - Clément J. Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga; Mahajanga, 401, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga; Mahajanga, 401, Madagascar
| | | | | | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center; Houston, Texas, 77030, USA
| | | | - Joe H. Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center; Houston, Texas, 77030, USA
| | - Eduardo Fernandez-Duque
- Yale University; New Haven, Connecticut, 06520, USA
- Universidad Nacional de Formosa, Argentina Fundacion ECO, Formosa, Argentina
| | | | | | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences; Kunming, Yunnan, 650223, China
| | - Long Zhou
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences; Kunming, Yunnan, 650223, China
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen; Copenhagen, DK-2100, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center; 1369 West Wenyi Road, Hangzhou, 311121, China
- Women’s Hospital, School of Medicine, Zhejiang University; 1 Xueshi Road, Shangcheng District, Hangzhou, 310006, China
| | - Julius D. Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Head Office; P.O.Box 661, Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health; 17493 Greifswald - Isle of Riems, Germany
| | - Minh D. Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University; Hanoi, 100000, Vietnam
| | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart; 70191 Stuttgart, Germany
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Pg. Luís Companys 23, Barcelona, 08010, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology; Av. Doctor Aiguader, N88, Barcelona, 08003, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation; C. Wellington 30, Barcelona, 08005, Spain
| | - Thomas Batallion
- Bioinformatics Research Centre, Aarhus University; Aarhus, 8000, Denmark
| | - Tilo Nadler
- Cuc Phuong Commune; Nho Quan District, Ninh Binh Province, 430000, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Jessica Lee
- Mandai Nature; 80 Mandai Lake Road, Singapore 729826, Republic of Singapore
| | - Patrick Tan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM); Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School; Singapore 168582, Republic of Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM); Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School; Singapore 168582, Republic of Singapore
- SingHealth Duke-NUS Genomic Medicine Centre; Singapore 168582, Republic of Singapore
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland; Chambers Street, Edinburgh, EH1 1JF, UK
- School of Geosciences, University of Edinburgh; Drummond Street, Edinburgh, EH8 9XP, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research; 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen; 37077 Göttingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
- Universitat Pompeu Fabra, Pg. Luís Companys 23, Barcelona, 08010, Spain
| | - Amanda Melin
- Leibniz Science Campus Primate Cognition; 37077 Göttingen, Germany
- Department of Anthropology & Archaeology and Department of Medical Genetics
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University; SE-75236, Uppsala, Sweden
- Alberta Children’s Hospital Research Institute; University of Calgary; 2500 University Dr NW T2N 1N4, Calgary, Alberta, Canada
| | | | - Robin M. D. Beck
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR); Ghaziabad, 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology; Hyderabad, 500007, India
| | - Christian Roos
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh; Edinburgh, EH8 9XP, UK
| | - Jean P. Boubli
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Monkol Lek
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research; Kellnerweg 4, 37077 Göttingen, Germany
| | - Shamil Sunyaev
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- Department of Genetics, Yale School of Medicine; New Haven, Connecticut, 06520, USA
| | - Anne O’Donnell
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Heidi Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Jinbo Xu
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
- Toyota Technological Institute at Chicago; Chicago, Illinois, 60637, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, Texas, 77030, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Pg. Luís Companys 23, Barcelona, 08010, Spain
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
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11
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Ximenes AM, Machado VN, Hernandez-Ruz EJ, de Lima Muniz F, Hrbek T, Farias IP. Multilocus approach reveals distinct evolutionary units of the South American apapa Pellona flavipinnis (Valenciennes, 1837) (Clupeiformes, Pristigasteridae). J Fish Biol 2023. [PMID: 37013734 DOI: 10.1111/jfb.15395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 04/03/2023] [Indexed: 05/25/2023]
Abstract
The discovery and characterization of cryptic diversity is important for conservation and management, especially for ichthyofauna, whose diversity is underestimated and understudied. Cryptic diversity is especially common in widely distributed species, and Pellona flavipinnis is one such species. Thus, the aim of the present study was to investigate and test whether P. flavipinnis harbours cryptic diversity. In this study we used the COI and control region sequences and microsatellite loci of 86-114 specimens from 11-12 locations throughout the Amazon basin, depending on the molecular marker used. We also included two COI GenBank sequences from the type locality of the species, the Paraná River. The results from COI sequences showed that P. flavipinnis from the Amazon basin presented two spatially structured lineages differentiated from P. flavipinnis from the Paraná River by 10.6%-9.8% (depending on the lineages) and 45 mutational steps. The genetic distance between the Amazon lineages was 2.4% using COI, with high population differentiation values (ФST = 0.8686 and ФST = 0.8483 for COI and control region, respectively). Among the five species delimitation methods employed, three indicated two lineages in P. flavipinnis in the Amazon basin, and all five methods indicated that the Amazonian lineages are different from that of Paraná. Results from microsatellite loci also showed that P. flavipinnis from the Amazon basin is composed of two evolutionary units. The results of 13 morphometric measurements indicated that there are no differences in shape between the P. flavipinnis lineages in the Amazon basin. The present findings suggest that there are two sympatric lineages of P. flavipinnis in the Amazon basin.
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Affiliation(s)
- Aline Mourão Ximenes
- Laboratório de Evolução e Genética Animal (LEGAL), Departamento de Genética, Universidade Federal do Amazonas (UFAM), Av. General Rodrigo Octávio Jordão Ramos, Manaus, Brazil
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo, Manaus, Brazil
| | - Valéria Nogueira Machado
- Laboratório de Evolução e Genética Animal (LEGAL), Departamento de Genética, Universidade Federal do Amazonas (UFAM), Av. General Rodrigo Octávio Jordão Ramos, Manaus, Brazil
| | - Emil José Hernandez-Ruz
- Laboratório de Zoologia, Programa de Pós-Graduação em Biodiversidade e Conservação, Universidade Federal do Pará (UFPA), R. Cel. José Porfírio, Esplanada do Xingu, Altamira, Brazil
| | - Fábio de Lima Muniz
- Laboratório de Evolução e Genética Animal (LEGAL), Departamento de Genética, Universidade Federal do Amazonas (UFAM), Av. General Rodrigo Octávio Jordão Ramos, Manaus, Brazil
- Instituto de Ciências Exatas e Naturais (ICEN), Universidade Federal de Rondonópolis (UFR), Rondonópolis, Brazil
| | - Tomas Hrbek
- Laboratório de Evolução e Genética Animal (LEGAL), Departamento de Genética, Universidade Federal do Amazonas (UFAM), Av. General Rodrigo Octávio Jordão Ramos, Manaus, Brazil
- Biology Department, Trinity University, San Antonio, Texas, USA
| | - Izeni Pires Farias
- Laboratório de Evolução e Genética Animal (LEGAL), Departamento de Genética, Universidade Federal do Amazonas (UFAM), Av. General Rodrigo Octávio Jordão Ramos, Manaus, Brazil
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12
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Lopes GP, Rohe F, Bertuol F, Polo E, Lima IJ, Valsecchi J, Santos TCM, Nash SD, da Silva MNF, Boubli JP, Farias IP, Hrbek T. Taxonomic review of Saguinus mystax (Spix, 1823) (Primates, Callitrichidae), and description of a new species. PeerJ 2023; 11:e14526. [PMID: 36647446 PMCID: PMC9840391 DOI: 10.7717/peerj.14526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 11/15/2022] [Indexed: 01/13/2023] Open
Abstract
Although the Amazon has the greatest diversity of primates, there are still taxonomic uncertainties for many taxa, such as the species of the Saguinus mystax group. The most geographically broadly distributed and phenotypically diverse species in this group is S. mystax, and its phenotypic diversity has been recognized as three subspecies-S. mystax mystax, S. mystax pileatus and S. mystax pluto-with non-overlapping geographic distributions. In this sense, we carried out an extensive field survey in their distribution areas and used a framework of taxonomic hypothesis testing of genomic data combined with an integrative taxonomic decision-making framework to carry out a taxonomic revision of S. mystax. Our tests supported the existence of three lineages/species. The first species corresponds to Saguinus mystax mystax from the left bank of the Juruá River, which was raised to the species level, and we also discovered and described animals from the Juruá-Tefé interfluve previously attributed to S. mystax mystax as a new species. The subspecies S. m. pileatus and S. m. pluto are recognized as a single species, under a new nomenclatural combination. However, given their phenotypic distinction and allopatric distribution, they potentially are a manifestation of an early stage of speciation, and therefore we maintain their subspecific designations.
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Affiliation(s)
- Gerson Paulino Lopes
- Programa em Pós-Graduação em Zoologia, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil,Grupo de Pesquisa em Ecologia e Conservação de Primatas, Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas, Brazil,Laboratório de Evolução e Genética Animal/Departamento de Genética/Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil,Grupo de Pesquisa em Ecologia de Vertebrados Terrestres, Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas, Brazil
| | - Fábio Rohe
- Laboratório de Evolução e Genética Animal/Departamento de Genética/Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil,Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Fabrício Bertuol
- Laboratório de Evolução e Genética Animal/Departamento de Genética/Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | - Erico Polo
- Laboratório de Evolução e Genética Animal/Departamento de Genética/Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | - Ivan Junqueira Lima
- Grupo de Pesquisa em Ecologia de Vertebrados Terrestres, Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas, Brazil,Programa de Pós-Graduação em Ecologia Aplicada, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - João Valsecchi
- Grupo de Pesquisa em Ecologia e Conservação de Primatas, Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas, Brazil,Grupo de Pesquisa em Ecologia de Vertebrados Terrestres, Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas, Brazil,Rede de Pesquisa em Diversidade, Conservação e Uso da Fauna da Amazônia, Manaus, Amazonas, Brazil,Comunidad de Manejo de Fauna Silvestre en América Latina, Iquitos, Peru
| | - Tamily Carvalho Melo Santos
- Grupo de Pesquisa em Ecologia de Vertebrados Terrestres, Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas, Brazil
| | - Stephen D. Nash
- Department of Anatomical Sciences/Health Sciences Center, Stony Brook University, New York, United States of America
| | | | - Jean P. Boubli
- Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil,School of Science, Engineering and the Environment, University of Salford, Salford, United Kingdom
| | - Izeni Pires Farias
- Programa em Pós-Graduação em Zoologia, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil,Laboratório de Evolução e Genética Animal/Departamento de Genética/Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | - Tomas Hrbek
- Programa em Pós-Graduação em Zoologia, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil,Laboratório de Evolução e Genética Animal/Departamento de Genética/Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil,Department of Biology, Trinity University, San Antonio, Texas, United States
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13
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Fouquet A, Réjaud A, Rodrigues MT, Ron SR, Chaparro JC, Osorno M, Werneck FP, Hrbek T, Lima AP, Camacho-Badani T, Jaramillo-Martinez AF, Chave J. Diversification of the Pristimantis conspicillatus group (Anura: Craugastoridae) within distinct neotropical areas throughout the Neogene. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2130464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Antoine Fouquet
- Laboratoire Evolution et Diversité Biologique, UMR 5174, CNRS, IRD, Université Paul Sabatier, Bâtiment 4R1, 118 Route de Narbonne, Toulouse, 31077, France
| | - Alexandre Réjaud
- Laboratoire Evolution et Diversité Biologique, UMR 5174, CNRS, IRD, Université Paul Sabatier, Bâtiment 4R1, 118 Route de Narbonne, Toulouse, 31077, France
| | - Miguel T. Rodrigues
- Departamento de Zoologia, Universidade de São Paulo Instituto de Biociências, São Paulo, SP, Brazil
| | - Santiago R. Ron
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Juan C. Chaparro
- Museo de Biodiversidad del Perú, Urbanización Mariscal Gamarra A-61, Zona 2, Cusco, Peru
- Museo de Historia Natural de la Universidad Nacional de San Antonio Abad del Cusco, Paraninfo Universitario (Plaza de Armas s/n), Cusco, Perú
| | - Mariela Osorno
- Instituto Amazónico de Investigaciones Científicas SINCHI, Sede enlace. Calle 20 # 5-44, Bogotá, Colombia
| | - Fernanda P. Werneck
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Avenida André Araújo 2936, Manaus, 69080-971, AM, Brazil
| | - Tomas Hrbek
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, 69080-900, AM, Brazil
| | - Albertina P. Lima
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Avenida André Araújo 2936, Manaus, 69080-971, AM, Brazil
| | | | - Andres F. Jaramillo-Martinez
- Laboratório de Sistemática de Vertebrados, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga 6681, Prédio 40, sala 110, Porto Alegre, 90619-900, RS, Brazil
| | - Jérôme Chave
- Laboratoire Evolution et Diversité Biologique, UMR 5174, CNRS, IRD, Université Paul Sabatier, Bâtiment 4R1, 118 Route de Narbonne, Toulouse, 31077, France
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14
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Campos Z, Muniz F, Mourão G, Magnusson WE, Farias IP, Hrbek T. Geographic variation in colour and spot patterns in Dwarf Caiman, Paleosuchus palpebrosus (Cuvier, 1807) in Brazil. AMPHIBIA-REPTILIA 2022. [DOI: 10.1163/15685381-bja10104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Colour variation in crocodilians is associated with size, environment and genetic structure, but little is known about colour variation in the genus Paleosuchus (Alligatoridae). Different genetic lineages of Paleosuchus palpebrosus (Dwarf caiman) occupy different environments throughout the species extensive distribution, and all are cryptically coloured. We captured 187 P. palpebrosus and recorded their head colour from four genetically distinct geographic clades between 2008 and 2019. Additionally, we determined the jaw and belly spot pattern of a subsample of 95 individuals (22–109 cm snout-vent length). PERMANCOVA was used to investigate the relationships between head colour and spot patterns, to the caiman size, sex, and geographic lineage, as well as ambient temperature. Variation in head colour, and jaw and belly spot patterns, were related to genetic lineage, snout-vent length and temperature, but the model explained only ∼45.4% of the variance in the data. Sex was not significantly related to the head colour, or jaw and belly spot patterns. Dwarf caimans inhabiting cooler climates tend to be darker than individuals from warmer areas, and individuals from the “Cerrado-Pantanal” and “Bolivia” lineages generally darker than the “Amazon” and “Madeira” lineages. However, individuals of a given size in different lineages overlap greatly in colour patterns and colour alone could not be used to distinguish lineages. The Natterer’s hypothesis of head-colour as diagnose from “Cerrado-Pantanal” lineage, cannot be completely accepted according our quantitative analysis, although there are a variation in the geographic distribution of these phenotypic traits, and the “Cerrado-Pantanal” lineage had been the most distinct among the lineages.
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Affiliation(s)
- Zilca Campos
- Laboratório de vida Selvagem, Embrapa: Empresa Brasileira de Pesquisa Agropecuaria, Embrapa Pantanal CP 109, Corumbá, MS, 79320-900, Brazil
| | - Fábio Muniz
- Instituto de ciências exatas e naturais (ICEN), Universidade Federal de Rondonópolis (UFR), Av. das estudantes, 5055, Cidade Universitária, Rondonópolis, MT 78736-900, Brazil
| | - Guilherme Mourão
- Laboratório de vida Selvagem, Embrapa: Empresa Brasileira de Pesquisa Agropecuaria, Embrapa Pantanal CP 109, Corumbá, MS, 79320-900, Brazil
| | - William E. Magnusson
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisa da Amazônia, CP 2223, Manaus, AM, 69080-971, Brazil
| | - Izeni P. Farias
- Laboratório de Evolução e Genética Animal, Universidade Federal do Amazonas, Manaus, AM, Brazil
| | - Tomas Hrbek
- Laboratório de Evolução e Genética Animal, Universidade Federal do Amazonas, Manaus, AM, Brazil
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15
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Janiak MC, Silva FE, Beck RMD, de Vries D, Kuderna LFK, Torosin NS, Melin AD, Marquès-Bonet T, Goodhead IB, Messias M, da Silva MNF, Sampaio I, Farias IP, Rossi R, de Melo FR, Valsecchi J, Hrbek T, Boubli JP. 205 newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates. Mol Ecol 2022; 31:3888-3902. [PMID: 35638312 PMCID: PMC9546496 DOI: 10.1111/mec.16554] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/06/2022] [Accepted: 05/20/2022] [Indexed: 12/02/2022]
Abstract
Mitochondrial DNA remains a cornerstone for molecular ecology, especially for study species from which high‐quality tissue samples cannot be easily obtained. Methods using mitochondrial markers are usually reliant on reference databases, but these are often incomplete. Furthermore, available mitochondrial genomes often lack crucial metadata, such as sampling location, limiting their utility for many analyses. Here, we assembled 205 new mitochondrial genomes for platyrrhine primates, most from the Amazon and with known sampling locations. We present a dated mitogenomic phylogeny based on these samples along with additional published platyrrhine mitogenomes, and use this to assess support for the long‐standing riverine barrier hypothesis (RBH), which proposes that river formation was a major driver of speciation in Amazonian primates. Along the Amazon, Negro, and Madeira rivers, we found mixed support for the RBH. While we identified divergences that coincide with a river barrier, only some occur synchronously and also overlap with the proposed dates of river formation. The most compelling evidence is for the Amazon river potentially driving speciation within bearded saki monkeys (Chiropotes spp.) and within the smallest extant platyrrhines, the marmosets and tamarins. However, we also found that even large rivers do not appear to be barriers for some primates, including howler monkeys (Alouatta spp.), uakaris (Cacajao spp.), sakis (Pithecia spp.), and robust capuchins (Sapajus spp.). Our results support a more nuanced, clade‐specific effect of riverine barriers and suggest that other evolutionary mechanisms, besides the RBH and allopatric speciation, may have played an important role in the diversification of platyrrhines.
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Affiliation(s)
- Mareike C Janiak
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom
| | - Felipe E Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Brazil.,Department of Evolutionary Biology and Ecology, Université Libre de Bruxelles, Belgium
| | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom
| | - Lukas F K Kuderna
- Ilumina Inc., Hayward, CA, USA.,Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
| | - Nicole S Torosin
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Amanda D Melin
- Department of Anthropology & Archaeology and Department of Medical Genetics, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute, Calgary, AB, Canada
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Cerdanyola del Vallès, Barcelona, Spain
| | - Ian B Goodhead
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom
| | - Mariluce Messias
- Department of Biology, Universidade Federal de Rondônia, Porto Velho, Brazil
| | - Maria N F da Silva
- Coleção de Mamíferos, Instituto Nacional de Pesquisas da Amazônia, Brazil
| | | | - Izeni P Farias
- Laboratory of Evolution and Animal Genetics, Universidade Federal do Amazonas, Brazil
| | - Rogerio Rossi
- Instituto de Biociências, Universidade Federal do Mato Grosso, Brazil
| | - Fabiano R de Melo
- Department of Forestry Engineering, Universidade Federal de Viçosa, Brazil
| | - João Valsecchi
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Brazil
| | - Tomas Hrbek
- Department of Biology, Trinity University, San Antonio, TX, USA
| | - Jean P Boubli
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom.,Coleção de Mamíferos, Instituto Nacional de Pesquisas da Amazônia, Brazil
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16
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Fouquet A, Cornuault J, Rodrigues MT, Werneck FP, Hrbek T, Acosta-Galvis AR, Massemin D, J. R. Kok P, Ernst R. Diversity, biogeography and reproductive evolution in the genus Pipa (Amphibia: Anura: Pipidae). Mol Phylogenet Evol 2022; 170:107442. [DOI: 10.1016/j.ympev.2022.107442] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/22/2021] [Accepted: 02/16/2022] [Indexed: 11/29/2022]
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17
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Martins-Junior AM, Sampaio I, Silva A, Boubli J, Hrbek T, Farias I, Ruiz-García M, Schneider H. Out of the shadows: Multilocus systematics and biogeography of night monkeys suggest a Central Amazonian origin and a very recent widespread southeastward expansion in South America. Mol Phylogenet Evol 2022; 170:107426. [DOI: 10.1016/j.ympev.2022.107426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 12/26/2021] [Accepted: 01/20/2022] [Indexed: 10/19/2022]
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18
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Escobar L. MD, Farias IP, Hrbek T. Genetic comparison of populations of Piaractus brachypomus and P. orinoquensis (Characiformes: Serrasalmidae) of the Amazon and Orinoco basins. Neotrop ichthyol 2022. [DOI: 10.1590/1982-0224-2022-0056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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19
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Ximenes AM, Bittencourt PS, Machado VN, Hrbek T, Farias IP. Mapping the hidden diversity of the Geophagus sensu stricto species group (Cichlidae: Geophagini) from the Amazon basin. PeerJ 2021; 9:e12443. [PMID: 34909270 PMCID: PMC8641480 DOI: 10.7717/peerj.12443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/15/2021] [Indexed: 11/20/2022] Open
Abstract
South American freshwater ichthyofauna is taxonomically the most diverse on the planet, yet its diversity is still vastly underestimated. The Amazon basin alone holds more than half of this diversity. The evidence of this underestimation comes from the backlog of morphologically distinct, yet undescribed forms deposited in museum collections, and from DNA-based inventories which consistently identify large numbers of divergent lineages within even well-studied species groups. In the present study, we investigated lineage diversity within the Geophagus sensu stricto species group. To achieve these objectives, we analyzed 337 individuals sampled from 77 locations within and outside the Amazon basin representing 10 nominal and six morphologically distinct but undescribed species. We sequenced the mitochondrial cytochrome c oxidase subunit I (COI) and delimited lineages using four different single-locus species discovery methods (mPTP-15 lineages; LocMin-14 lineages; bGMYC-18 lineages; and GMYC-30 lineages). The six morphologically distinct but undescribed species were also delimited by the majority of the species discovery methods. Five of these lineages are restricted to a single collection site or a watershed and their habitats are threatened by human activities such as deforestation, agricultural activities and construction of hydroelectric plants. Our results also highlight the importance of combining DNA and morphological data in biodiversity assessment studies especially in taxonomically diverse tropical biotas.
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Affiliation(s)
- Aline Mourão Ximenes
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil.,Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Pedro Senna Bittencourt
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | - Valéria Nogueira Machado
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | - Tomas Hrbek
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil.,Biology Department, Trinity University, San Antonio, Texas, USA
| | - Izeni Pires Farias
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
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20
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Kobzar Y, Fatyeyeva K, Lobko Y, Yakovlev Y, Hrbek T, Marais S. New ionic liquid-based polyoxadiazole electrolytes for hydrogen middle- and high-temperature fuel cells. J Memb Sci 2021. [DOI: 10.1016/j.memsci.2021.119774] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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21
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Boubli JP, Janiak MC, Porter LM, de la Torre S, Cortés-Ortiz L, Da Silva MNF, Rylands AB, Nash S, Bertuol F, Byrne H, Silva FE, Rohe F, de Vries D, Beck RMD, Ruiz-Gartzia I, Kuderna LFK, Marques-Bonet T, Hrbek T, Farias IP, Van Heteren AH, Roos C. Ancient DNA of the pygmy marmoset type specimen Cebuella pygmaea (Spix, 1823) resolves a taxonomic conundrum. Zool Res 2021; 42:761-771. [PMID: 34643070 PMCID: PMC8645880 DOI: 10.24272/j.issn.2095-8137.2021.143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The pygmy marmoset, the smallest of the anthropoid primates, has a broad distribution in Western Amazonia. Recent studies using molecular and morphological data have identified two distinct species separated by the Napo and Solimões-Amazonas rivers. However, reconciling this new biological evidence with current taxonomy, i.e., two subspecies, Cebuella pygmaea pygmaea (Spix, 1823) and Cebuella pygmaea niveiventris (Lönnberg, 1940), was problematic given the uncertainty as to whether Spix’s pygmy marmoset (Cebuella pygmaea pygmaea) was collected north or south of the Napo and Solimões-Amazonas rivers, making it unclear to which of the two newly revealed species the name pygmaea would apply. Here, we present the first molecular data from Spix’s type specimen of Cebuella pygmaea, as well as novel mitochondrial genomes from modern pygmy marmosets sampled near the type locality (Tabatinga) on both sides of the river. With these data, we can confirm the correct names of the two species identified, i.e., C. pygmaea for animals north of the Napo and Solimões-Amazonas rivers and C. niveiventris for animals south of these two rivers. Phylogenetic analyses of the novel genetic data placed into the context of cytochrome b gene sequences from across the range of pygmy marmosets further led us to re-evaluate the geographical distribution for the two Cebuella species. We dated the split of these two species to 2.54 million years ago. We discuss additional, more recent, subdivisions within each lineage, as well as potential contact zones between the two species in the headwaters of these rivers.
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Affiliation(s)
- Jean P Boubli
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK.,Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas 69060-001, Brazil. E-mail:
| | - Mareike C Janiak
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Leila M Porter
- Department of Anthropology, Northern Illinois University, DeKalb, IL 60115-2828, USA
| | - Stella de la Torre
- College of Biological and Environmental Sciences, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Liliana Cortés-Ortiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maria N F Da Silva
- Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas 69060-001, Brazil
| | | | - Stephen Nash
- Global Wildlife Conservation, Austin, TX 78767, USA
| | - Fabrício Bertuol
- Laboratório de Evolução e Genética Animal, Universidade Federal do Amazonas, Manaus, Amazonas 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City, UT 84112, USA
| | - Felipe E Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Tefé, Amazonas 69553-225, Brazil
| | - Fabio Rohe
- Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas 69060-001, Brazil
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Irune Ruiz-Gartzia
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona 08002, Spain
| | - Lukas F K Kuderna
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona 08002, Spain
| | - Tomas Marques-Bonet
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona 08002, Spain
| | - Tomas Hrbek
- Laboratório de Evolução e Genética Animal, Universidade Federal do Amazonas, Manaus, Amazonas 69080-900, Brazil.,Department of Biology, Trinity University, San Antonio, TX 78212, USA
| | - Izeni P Farias
- Laboratório de Evolução e Genética Animal, Universidade Federal do Amazonas, Manaus, Amazonas 69080-900, Brazil
| | - Anneke H Van Heteren
- Bavarian State Collection of Zoology, Zoologische Staatssammlung München, Staatliche Naturkundliche Sammlungen Bayerns, Munich 81247, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, Munich 80333, Germany.,Department Biologie II, Ludwig-Maximilians-Universität München, Munich 82152, Germany
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
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22
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Costa-Araújo R, Silva-Jr JS, Boubli JP, Rossi RV, Canale GR, Melo FR, Bertuol F, Silva FE, Silva DA, Nash SD, Sampaio I, Farias IP, Hrbek T. An integrative analysis uncovers a new, pseudo-cryptic species of Amazonian marmoset (Primates: Callitrichidae: Mico) from the arc of deforestation. Sci Rep 2021; 11:15665. [PMID: 34341361 PMCID: PMC8328995 DOI: 10.1038/s41598-021-93943-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/23/2021] [Indexed: 12/03/2022] Open
Abstract
Amazonia has the richest primate fauna in the world. Nonetheless, the diversity and distribution of Amazonian primates remain little known and the scarcity of baseline data challenges their conservation. These challenges are especially acute in the Amazonian arc of deforestation, the 2500 km long southern edge of the Amazonian biome that is rapidly being deforested and converted to agricultural and pastoral landscapes. Amazonian marmosets of the genus Mico are little known endemics of this region and therefore a priority for research and conservation efforts. However, even nascent conservation efforts are hampered by taxonomic uncertainties in this group, such as the existence of a potentially new species from the Juruena-Teles Pires interfluve hidden within the M. emiliae epithet. Here we test if these marmosets belong to a distinct species using new morphological, phylogenomic, and geographic distribution data analysed within an integrative taxonomic framework. We discovered a new, pseudo-cryptic Mico species hidden within the epithet M. emiliae, here described and named after Horacio Schneider, the pioneer of molecular phylogenetics of Neotropical primates. We also clarify the distribution, evolutionary and morphological relationships of four other Mico species, bridging Linnean, Wallacean, and Darwinian shortfalls in the conservation of primates in the Amazonian arc of deforestation.
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Affiliation(s)
- Rodrigo Costa-Araújo
- Museu Paraense Emílio Goeldi, Mastozoology Collection, Belém, 66077-830, Brazil.
- Laboratory of Evolution and Animal Genetics, Federal University of Amazonas, Manaus, 69077-000, Brazil.
| | - José S Silva-Jr
- Museu Paraense Emílio Goeldi, Mastozoology Collection, Belém, 66077-830, Brazil
| | - Jean P Boubli
- School of Science, Engineering and Environment, University of Salford, Salford, M54WT, UK
| | - Rogério V Rossi
- Institute of Biosciences, Federal University of Mato Grosso, Cuiabá, 78060-900, Brazil
| | - Gustavo R Canale
- Institute of Natural, Human and Social Sciences, Federal University of Mato Grosso, Sinop, 78557-267, Brazil
| | - Fabiano R Melo
- Department of Forest Engineering, Federal University of Viçosa, Viçosa, 36570-900, Brazil
| | - Fabrício Bertuol
- Laboratory of Evolution and Animal Genetics, Federal University of Amazonas, Manaus, 69077-000, Brazil
| | - Felipe E Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Tefé, 69553-225, Brazil
| | - Diego A Silva
- Graduate Program in Ecology and Conservation, State University of Mato Grosso, Nova Xavantina, 78690-000, Brazil
| | - Stephen D Nash
- Departments of Anatomical Sciences and Art, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Iracilda Sampaio
- Institute of Coastal Studies, Federal University of Pará, Bragança, 68600-000, Brazil
| | - Izeni P Farias
- Laboratory of Evolution and Animal Genetics, Federal University of Amazonas, Manaus, 69077-000, Brazil
| | - Tomas Hrbek
- Laboratory of Evolution and Animal Genetics, Federal University of Amazonas, Manaus, 69077-000, Brazil.
- Department of Biology, Trinity University, San Antonio, 78212, USA.
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23
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Fouquet A, Marinho P, Réjaud A, Carvalho TR, Caminer MA, Jansen M, Rainha RN, Rodrigues MT, Werneck FP, Lima AP, Hrbek T, Giaretta AA, Venegas PJ, Chávez G, Ron S. Systematics and biogeography of the Boana albopunctata species group (Anura, Hylidae), with the description of two new species from Amazonia. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1873869] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Antoine Fouquet
- Laboratoire Evolution et Diversité Biologique, UMR 5174, CNRS, IRD, Université Paul Sabatier, Bâtiment 4R1 31062 cedex 9, 118 Route de Narbonne, Toulouse, 31077, France
| | - Pedro Marinho
- Laboratório de Anuros Neotropicais, Instituto de Ciências Exatas e Naturais do Pontal, Universidade Federal de Uberlândia, Ituiutaba, MG, Brazil
| | - Alexandre Réjaud
- Laboratoire Evolution et Diversité Biologique, UMR 5174, CNRS, IRD, Université Paul Sabatier, Bâtiment 4R1 31062 cedex 9, 118 Route de Narbonne, Toulouse, 31077, France
| | - Thiago R. Carvalho
- Laboratório de Herpetologia, Departamento de Biodiversidade e Centro de Aquicultura, I.B., Universidade Estadual Paulista, Rio Claro, SP, Brazil
| | - Marcel A. Caminer
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Germany
| | - Martin Jansen
- Department of Terrestrial Zoology, Research Institute and Nature Museum Senckenberg, Frankfurt, Germany
| | - Raíssa N. Rainha
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Manaus, AM, Brazil
| | - Miguel T. Rodrigues
- Departamento de Zoologia, Universidade de São Paulo, Instituto de Biociências, São Paulo, SP, Brazil
| | - Fernanda P. Werneck
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Manaus, AM, Brazil
| | - Albertina P. Lima
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Manaus, AM, Brazil
| | - Tomas Hrbek
- Departamento de Genética, Universidade Federal do Amazonas, Manaus, AM, Brazil
| | - Ariovaldo A. Giaretta
- Laboratório de Anuros Neotropicais, Instituto de Ciências Exatas e Naturais do Pontal, Universidade Federal de Uberlândia, Ituiutaba, MG, Brazil
| | | | | | - Santiago Ron
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
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24
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DE Almeida AP, Moraes LJCL, Rojas RR, Roberto IJ, Carvalho VTDE, Ávila RW, Frazão L, Silva AAA, Menin M, Werneck FP, Hrbek T, Farias IP, Gordo M. Phylogenetic relationships of the poorly known treefrog Boana hobbsi (Cochran amp; Goin, 1970) (Anura: Hylidae), systematic implications and remarks on morphological variations and geographic distribution. Zootaxa 2021; 4933:zootaxa.4933.3.1. [PMID: 33756784 DOI: 10.11646/zootaxa.4933.3.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Indexed: 11/04/2022]
Abstract
Boana hobbsi is a poorly known hylid frog currently placed within the Boana punctata group. Yet, morphological, ecological and bioacoustic traits do not support this placement, with no molecular data being available to date to test this hypothesis. Based on newly collected mitochondrial DNA sequences, morphological data review and field observations, we provide new insight into the phylogenetic relationships, morphological variations and geographic distribution of B. hobbsi. Our findings reveal that B. hobbsi is nested (with strong support) within the Boana benitezi group, recovering once more a polyphyletic Boana punctata group. Supported by this new genetic, morphological and ecological evidence, we propose a new taxonomic arrangement which includes B. hobbsi as a member of the Boana benitezi group. Furthermore, we emphasize the importance of conducting biological inventories in remote Amazonian areas, where many taxonomic and geographic knowledge gaps persist with regards to Amphibian diversity.
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Affiliation(s)
- Alexandre P DE Almeida
- Universidade Federal do Amazonas, Instituto de Ciências Biológicas, Programa de Pós-Graduação em Zoologia, Avenida General Rodrigo Otávio J. Ramos 6200, 69080-900, Manaus, Amazonas, Brazil. Universidade Federal do Amazonas, Laboratório de Evolução e Genética Animal, Departamento de Genética, Avenida General Rodrigo Otávio J. Ramos 6200, Japiim, 69080-900, Manaus, Amazonas, Brazil..
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25
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Fouquet A, Leblanc K, Framit M, Réjaud A, Rodrigues MT, Castroviejo-Fisher S, Peloso PLV, Prates I, Manzi S, Suescun U, Baroni S, Moraes LJCL, Recoder R, de Souza SM, Dal Vecchio F, Camacho A, Ghellere JM, Rojas-Runjaic FJM, Gagliardi-Urrutia G, de Carvalho VT, Gordo M, Menin M, Kok PJR, Hrbek T, Werneck FP, Crawford AJ, Ron SR, Mueses-Cisneros JJ, Rojas Zamora RR, Pavan D, Ivo Simões P, Ernst R, Fabre AC. Species diversity and biogeography of an ancient frog clade from the Guiana Shield (Anura: Microhylidae: Adelastes, Otophryne, Synapturanus) exhibiting spectacular phenotypic diversification. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa204] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Abstract
The outstanding biodiversity of the Guiana Shield has raised many questions about its origins and evolution. Frogs of the genera Adelastes, Otophryne and Synapturanus form an ancient lineage distributed mostly across this region. These genera display strikingly disparate morphologies and life-history traits. Notably, Synapturanus is conspicuously adapted to fossoriality and is the only genus within this group to have dispersed further into Amazonia. Moreover, morphological differences among Synapturanus species suggest different degrees of fossoriality that might be linked to their biogeographical history. Through integrative analysis of genetic, morphometric and acoustic data, we delimited 25 species in this clade, representing a fourfold increase. We found that the entire clade started to diversify ~55 Mya and Synapturanus ~30 Mya. Members of this genus probably dispersed three times out of the Guiana Shield both before and after the Pebas system, a wetland ecosystem occupying most of Western Amazonia during the Miocene. Using a three-dimensional osteological dataset, we characterized a high morphological disparity across the three genera. Within Synapturanus, we further characterized distinct phenotypes that emerged concomitantly with dispersals during the Miocene and possibly represent adaptations to different habitats, such as soils with different physical properties.
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Affiliation(s)
- Antoine Fouquet
- Laboratoire Evolution et Diversité Biologique, UMR 5174, CNRS, IRD, Université Paul Sabatier, Bâtiment 4R1 31062 cedex 9, 118 Route de Narbonne, Toulouse, France
| | - Killian Leblanc
- Laboratoire Evolution et Diversité Biologique, UMR 5174, CNRS, IRD, Université Paul Sabatier, Bâtiment 4R1 31062 cedex 9, 118 Route de Narbonne, Toulouse, France
| | - Marlene Framit
- Laboratoire Evolution et Diversité Biologique, UMR 5174, CNRS, IRD, Université Paul Sabatier, Bâtiment 4R1 31062 cedex 9, 118 Route de Narbonne, Toulouse, France
| | - Alexandre Réjaud
- Laboratoire Evolution et Diversité Biologique, UMR 5174, CNRS, IRD, Université Paul Sabatier, Bâtiment 4R1 31062 cedex 9, 118 Route de Narbonne, Toulouse, France
| | - Miguel T Rodrigues
- Universidade de São Paulo Instituto de Biociências, Departamento de Zoologia, São Paulo, SP, Brazil
| | - Santiago Castroviejo-Fisher
- Pontifícia Universidade Católica do Rio Grande do Sul, Laboratório de Sistemática de Vertebrados/Programa de Pós-Graduação em Ecologia e Evolução da Biodiversidade, Escola de Ciências da Saúde e da Vida, Porto Alegre, RS, Brazil
| | - Pedro L V Peloso
- Universidade Federal do Pará, Instituto de Ciências Biológicas, R. Augusto Corrêa, 1, Guamá, Belém, Pará, Brazil
| | - Ivan Prates
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Sophie Manzi
- Laboratoire Evolution et Diversité Biologique, UMR 5174, CNRS, IRD, Université Paul Sabatier, Bâtiment 4R1 31062 cedex 9, 118 Route de Narbonne, Toulouse, France
| | - Uxue Suescun
- Laboratoire Evolution et Diversité Biologique, UMR 5174, CNRS, IRD, Université Paul Sabatier, Bâtiment 4R1 31062 cedex 9, 118 Route de Narbonne, Toulouse, France
| | - Sabrina Baroni
- Universidade de São Paulo Instituto de Biociências, Departamento de Zoologia, São Paulo, SP, Brazil
| | - Leandro J C L Moraes
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Avenida André Araújo 2936, Manaus, AM, Brazil
| | - Renato Recoder
- Universidade de São Paulo Instituto de Biociências, Departamento de Zoologia, São Paulo, SP, Brazil
| | - Sergio Marques de Souza
- Universidade de São Paulo Instituto de Biociências, Departamento de Zoologia, São Paulo, SP, Brazil
| | - Francisco Dal Vecchio
- Universidade de São Paulo Instituto de Biociências, Departamento de Zoologia, São Paulo, SP, Brazil
| | - Agustín Camacho
- Universidade de São Paulo Instituto de Biociências, Departamento de Zoologia, São Paulo, SP, Brazil
| | - José Mario Ghellere
- Pontifícia Universidade Católica do Rio Grande do Sul, Laboratório de Sistemática de Vertebrados/Programa de Pós-Graduação em Ecologia e Evolução da Biodiversidade, Escola de Ciências da Saúde e da Vida, Porto Alegre, RS, Brazil
| | - Fernando J M Rojas-Runjaic
- Pontifícia Universidade Católica do Rio Grande do Sul, Laboratório de Sistemática de Vertebrados/Programa de Pós-Graduação em Ecologia e Evolução da Biodiversidade, Escola de Ciências da Saúde e da Vida, Porto Alegre, RS, Brazil
- Fundación La Salle de Ciencias Naturales, Museo de Historia Natural La Salle, Sección de Herpetología, Caracas, Venezuela
| | - Giussepe Gagliardi-Urrutia
- Pontifícia Universidade Católica do Rio Grande do Sul, Laboratório de Sistemática de Vertebrados/Programa de Pós-Graduação em Ecologia e Evolução da Biodiversidade, Escola de Ciências da Saúde e da Vida, Porto Alegre, RS, Brazil
- Peruvian Center for Biodiversity and Conservation (PCB&C), Iquitos, Peru
| | - Vinícius Tadeu de Carvalho
- Programa de Pós-Graduação em Diversidade Biológica e Recursos Naturais, Universidade Regional do Cariri, Rua Cel. Antônio Luiz, 1161, 63.105-000, Crato CE, Brazil
| | - Marcelo Gordo
- Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, AM, Brazil
| | - Marcelo Menin
- Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, AM, Brazil
| | - Philippe J R Kok
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Łódź, 12/16 Banacha Str., Łódź, Poland
| | - Tomas Hrbek
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, AM, Brazil
| | - Fernanda P Werneck
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Avenida André Araújo 2936, Manaus, AM, Brazil
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Santiago R Ron
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Jonh Jairo Mueses-Cisneros
- Corporación para el Desarrollo Sostenible del Sur de la Amazonia-CORPOAMAZONIA, Mocoa, Putumayo, Colombia
| | - Rommel Roberto Rojas Zamora
- Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, AM, Brazil
| | - Dante Pavan
- Ecosfera Consultoria e Pesquisa em Meio Ambiente LTDA. Rodovia BR-259 s/n, Fazenda Bela Vista, Itapina, ES, Brazil
| | - Pedro Ivo Simões
- Departamento de Zoologia, Universidade Federal de Pernambuco, Av. Professor Moraes Rego, S/N, Cidade Universitária, 50760-420, Recife, PE, Brazil
| | - Raffael Ernst
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Dresden, Germany
| | - Anne-Claire Fabre
- The Natural History Museum, London, UK
- Palaeontological Institute and Museum, University of Zurich, Zurich, Switzerland
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Buainain N, Canton R, Zuquim G, Tuomisto H, Hrbek T, Sato H, Ribas CC. Paleoclimatic evolution as the main driver of current genomic diversity in the widespread and polymorphic Neotropical songbird Arremon taciturnus. Mol Ecol 2020; 29:2922-2939. [PMID: 32623766 DOI: 10.1111/mec.15534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 06/04/2020] [Accepted: 06/18/2020] [Indexed: 01/27/2023]
Abstract
Several factors have been proposed as drivers of species diversification in the Neotropics, including environmental heterogeneity, the development of drainage systems and historical changes in forest distribution due to climatic oscillations. Here, we investigate which drivers contributed to the evolutionary history and current patterns of diversity of a polymorphic songbird (Arremon taciturnus) that is widely distributed in Amazonian and Atlantic forests as well as in Cerrado gallery and seasonally-dry forests. We use genomic, phenotypic and habitat heterogeneity data coupled with climatic niche modelling. Results suggest the evolutionary history of the species is mainly related to paleoclimatic changes, although changes in the strength of the Amazon river as a barrier to dispersal, current habitat heterogeneity and geographic distance were also relevant. We propose an ancestral distribution in the Guyana Shield, and recent colonization of areas south of the Amazon river at ~380 to 166 kya, and expansion of the distribution to southern Amazonia, Cerrado and the Atlantic Forest. Since then, populations south of the Amazon River have been subjected to cycles of isolation and possibly secondary contact due to climatic changes that affected habitat heterogeneity and population connectivity. Most Amazonian rivers are not associated with long lasting isolation of populations, but some might act as secondary barriers, susceptible to crossing under specific climatic conditions. Morphological variation, while stable in some parts of the distribution, is not a reliable indicator of genetic structure or phylogenetic relationships.
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Affiliation(s)
- Nelson Buainain
- Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, AM, Brazil
| | - Roberta Canton
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Gabriela Zuquim
- Department of Biology, University of Turku, Turun Yliopisto, Finland
| | - Hanna Tuomisto
- Department of Biology, University of Turku, Turun Yliopisto, Finland
| | - Tomas Hrbek
- Departmento de Genetica, Universidade Federal do Amazonas, Manaus, AM, Brazil
| | - Hiromitsu Sato
- Department of Earth Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Camila C Ribas
- Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, AM, Brazil
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Carneiro J, Sampaio I, Lima T, Silva-Júnior JDS, Farias I, Hrbek T, Valsecchi J, Boubli J, Schneider H. Phylogenetic relationships in the genus Cheracebus (Callicebinae, Pitheciidae). Am J Primatol 2020; 82:e23167. [PMID: 32652664 DOI: 10.1002/ajp.23167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/06/2020] [Accepted: 04/13/2020] [Indexed: 11/08/2022]
Abstract
Cheracebus is a new genus of New World primate of the family Pitheciidae, subfamily Callicebinae. Until recently, Cheracebus was classified as the torquatus species group of the genus Callicebus. The genus Cheracebus has six species: C. lucifer, C. lugens, C. regulus, C. medemi, C. torquatus, and C. purinus, which are all endemic to the Amazon biome. Before the present study, there had been no conclusive interpretation of the phylogenetic relationships among most of the Cheracebus species. The present study tests the monophyly of the genus and investigates the relationships among the different Cheracebus species, based on DNA sequencing of 16 mitochondrial and nuclear markers. The phylogenetic analyses were based on Maximum Likelihood, Bayesian Inference, and multispecies coalescent approaches. The divergence times and genetic distances between the Cheracebus taxa were also estimated. The analyses confirmed the monophyly of the genus and a well-supported topology, with the following arrangement: ((C. torquatus, C. lugens), (C. lucifer (C. purinus, C. regulus))). A well-differentiated clade was also identified within part of the geographic range of C. lugens, which warrants further investigation to confirm its taxonomic status.
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Affiliation(s)
- Jeferson Carneiro
- Genomics and Systems Biology Center, Universidade Federal do Para, Belem, Brazil.,Instituto de Estudos Costeiros, Universidade Federal do Para, Campus Universitario de Bragança, Bragança, Para, Brazil
| | - Iracilda Sampaio
- Genomics and Systems Biology Center, Universidade Federal do Para, Belem, Brazil.,Instituto de Estudos Costeiros, Universidade Federal do Para, Campus Universitario de Bragança, Bragança, Para, Brazil
| | - Thaynara Lima
- Instituto de Estudos Costeiros, Universidade Federal do Para, Campus Universitario de Bragança, Bragança, Para, Brazil
| | | | - Izeni Farias
- Laboratory of Evolution and Animal Genetics, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | - Tomas Hrbek
- Laboratory of Evolution and Animal Genetics, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | - João Valsecchi
- Instituto de Desenvolvimento Sustentável Mamirauá, Mamiraua Sustainable Development Reserve, Amazonas, Brazil
| | - Jean Boubli
- School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Horacio Schneider
- Genomics and Systems Biology Center, Universidade Federal do Para, Belem, Brazil.,Instituto de Estudos Costeiros, Universidade Federal do Para, Campus Universitario de Bragança, Bragança, Para, Brazil
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Roberto IJ, Bittencourt PS, Muniz FL, Hernández-Rangel SM, Nóbrega YC, Ávila RW, Souza BC, Alvarez G, Miranda-Chumacero G, Campos Z, Farias IP, Hrbek T. Unexpected but unsurprising lineage diversity within the most widespread Neotropical crocodilian genus Caiman (Crocodylia, Alligatoridae). SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1769222] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Igor J. Roberto
- Laboratory of Animal Genetics and Evolution (LEGAL), Federal University of Amazonas (UFAM), Manaus, AM, Brazil
- Post-Graduate Program in Zoology, Institute of Biological Sciences, Federal University of Amazonas (UFAM), Manaus, AM, Brazil
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Pedro S. Bittencourt
- Laboratory of Animal Genetics and Evolution (LEGAL), Federal University of Amazonas (UFAM), Manaus, AM, Brazil
| | - Fabio L. Muniz
- Laboratory of Animal Genetics and Evolution (LEGAL), Federal University of Amazonas (UFAM), Manaus, AM, Brazil
| | - Sandra M. Hernández-Rangel
- Laboratory of Animal Genetics and Evolution (LEGAL), Federal University of Amazonas (UFAM), Manaus, AM, Brazil
| | | | - Robson W. Ávila
- Department of Biology, Federal University of Ceará (UFC), Fortaleza, CE, Brazil
| | - Bruno C. Souza
- Chico Mendes Institute for Biodiversity Conservation (ICMBio), Boa Vista, RR, Brazil
| | - Gustavo Alvarez
- Wildlife Conservation Society (WCS), Bolivia Program, La Paz, Bolivia
| | | | - Zilca Campos
- Wildlife Laboratory, Brazilian Agricultural Research Corporation (EMBRAPA) Pantanal, Corumbá, MS, Brazil
| | - Izeni P. Farias
- Laboratory of Animal Genetics and Evolution (LEGAL), Federal University of Amazonas (UFAM), Manaus, AM, Brazil
| | - Tomas Hrbek
- Laboratory of Animal Genetics and Evolution (LEGAL), Federal University of Amazonas (UFAM), Manaus, AM, Brazil
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Vargas-Ramírez M, Caballero S, Morales-Betancourt MA, Lasso CA, Amaya L, Martínez JG, das Neves Silva Viana M, Vogt RC, Farias IP, Hrbek T, Campbell PD, Fritz U. Genomic analyses reveal two species of the matamata (Testudines: Chelidae: Chelus spp.) and clarify their phylogeography. Mol Phylogenet Evol 2020; 148:106823. [PMID: 32278863 DOI: 10.1016/j.ympev.2020.106823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 03/30/2020] [Accepted: 04/02/2020] [Indexed: 10/24/2022]
Abstract
The matamata is one of the most charismatic turtles on earth, widely distributed in northern South America. Debates have occurred over whether or not there should be two subspecies or species recognized due to its geographic variation in morphology. Even though the matamata is universally known, its natural history, conservation status and biogeography are largely unexplored. In this study we examined the phylogeographic differentiation of the matamata based on three mitochondrial DNA fragments (2168 bp of the control region, cytochrome oxidase subunit I, and the cytochrome b gene), one nuclear genomic DNA fragment (1068 bp of the R35 intron) and 1661 Single Nucleotide Polymorphisms (SNPs). Our molecular and morphological analyses revealed the existence of two distinct, genetically deeply divergent evolutionary lineages of matamatas that separated in the late Miocene (approximately 12.7 million years ago), corresponding well to the time when the Orinoco Basin was established. As a result of our analyses, we describe the genetically and morphologically highly distinct matamata from the Orinoco and Río Negro Basins and the Essequibo drainage as a species new to science (Chelus orinocensis sp. nov.). Chelus fimbriata sensu stricto is distributed in the Amazon Basin and the Mahury drainage. Additionally, the analyses revealed that each species displays phylogeographic differentiation. For C. orinocensis, there is moderate mitochondrial differentiation between the Orinoco and the Río Negro. For C. fimbriata, there is more pronounced differentiation matching different river systems. One mitochondrial clade was identified from the Amazon, Ucayali, and Mahury Rivers, and another one from the Madeira and Jaci Paraná Rivers. The C. orinocensis in the Essequibo and Branco Rivers have haplotypes that constitute a third clade clustering with C. fimbriata. Phylogenetic analyses of the R35 intron and SNP data link the matamatas from the Essequibo and Branco with the new species, suggesting past gene flow and old mitochondrial introgression. Chelus orinocensis is collected for the pet trade in Colombia and Venezuela. However, neither the extent of the harvest nor its impact are known. Hence, it is crucial to gather more information and to assess its exploitation throughout its distribution range to obtain a better understanding of its conservation status and to design appropriate conservation and management procedures. RESUMEN: La matamata es una de las tortugas más carismáticas del mundo, ampliamente distribuida en el norte de Sudamérica. Debido a su variación morfológica geográfica, se debate sobre el reconocimiento de dos subespecies o especies. A pesar de que la matamata es universalmente conocida, su historia natural, estado de conservación y biogeografía han sido muy poco estudiados. En este estudio examinamos la diferenciación filogeográfica de las matamatas en base a tres fragmentos de ADN mitocondrial (2168 pb de la región de control, la subunidad I del citocromo oxidasa y el gen del citocromo b), un fragmento de ADN genómico nuclear (1068 pb del intrón R35) y 1661 polimorfismos de nucleótido único (SNPs). Nuestros análisis moleculares y morfológicos revelaron la existencia de dos linajes evolutivos distintos de matamatas, genéticamente divergentes que se separaron en el Mioceno tardio (hace aproximadamente 12.7 millones de años), correspondiendo al tiempo en que se estableció la cuenca del Orinoco. Como resultado de nuestros análisis, describimos las genéticamente y morfológicamente distintas matamatas de las cuencas del Orinoco, Río Negro y Essequibo como una especie nueva para la ciencia (Chelus orinocensis sp. nov.). Chelus fimbriata sensu stricto se distribuye en la cuenca del Amazonas y en el drenaje del Mahury. Adicionalmente, los análisis revelaron que cada especie muestra diferenciación filogeográfica. Para C. orinocensis, hay una moderada diferenciación mitocondrial entre el Orinoco y el Río Negro. Para C. fimbriata, hay una diferenciación más pronunciada, concordando con los diferentes sistemas fluviales. Se identificó un clado de los ríos Amazonas, Ucayali y Mahury y otro de los ríos Madeira y Jaci Paraná. Las C. orinocensis de los ríos Essequibo y Branco tienen haplotipos que constituyen un tercer clado que se agrupa con C. fimbriata. Los análisis filogenéticos del intrón R35 y los datos de SNP asocian las matamatas de Essequibo y Branco con la nueva especie, sugiriendo flujo de genes pasado e introgresión mitocondrial antigua. Chelus orinocensis se colecta para el comercio de mascotas en Colombia y Venezuela. Sin embargo, ni se conoce el alcance de las colectas ni su impacto. Por lo tanto, es crucial recopilar más información y evaluar su explotación en todo su rango de distribución, comprender mejor su estado de conservación y para diseñar acciones apropiadas de conservación y manejo.
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Affiliation(s)
- Mario Vargas-Ramírez
- Estación de Biología Tropical Roberto Franco (EBTRF), Universidad Nacional de Colombia, Villavicencio, Colombia; Biodiversidad y Conservación Genética, Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia; Museum of Zoology, Senckenberg Dresden, A. B. Meyer Building, Dresden, Germany.
| | - Susana Caballero
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos-LEMVA, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - Mónica A Morales-Betancourt
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Programa Ciencias de la Biodiversidad, Línea de Recursos Hidrobiológicos, Pesqueros Continentales y Fauna Silvestre, Bogotá, Colombia
| | - Carlos A Lasso
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Programa Ciencias de la Biodiversidad, Línea de Recursos Hidrobiológicos, Pesqueros Continentales y Fauna Silvestre, Bogotá, Colombia
| | - Laura Amaya
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos-LEMVA, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - José Gregorio Martínez
- Grupo de Investigación Biociencias, Facultad de Ciencias de la Salud, Institución Universitaria Colegio Mayor de Antioquia, Medellín, Colombia; Laboratório de Evolução e Genética Animal, Departamento de Genetica, Universidade Federal do Amazonas, Manaus, Brazil
| | - Maria das Neves Silva Viana
- Laboratório de Evolução e Genética Animal, Departamento de Genetica, Universidade Federal do Amazonas, Manaus, Brazil
| | - Richard C Vogt
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Izeni Pires Farias
- Laboratório de Evolução e Genética Animal, Departamento de Genetica, Universidade Federal do Amazonas, Manaus, Brazil
| | - Tomas Hrbek
- Laboratório de Evolução e Genética Animal, Departamento de Genetica, Universidade Federal do Amazonas, Manaus, Brazil
| | - Patrick D Campbell
- Department of Life Sciences, Darwin Centre 1, Natural History Museum, London, UK
| | - Uwe Fritz
- Museum of Zoology, Senckenberg Dresden, A. B. Meyer Building, Dresden, Germany
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Bittencourt PS, Machado VN, Marshall BG, Hrbek T, Farias IP. Phylogenetic relationships of the neon tetras Paracheirodon spp. (Characiformes: Characidae: Stethaprioninae), including comments on Petitella georgiae and Hemigrammus bleheri. Neotrop ichthyol 2020. [DOI: 10.1590/1982-0224-2019-0109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
ABSTRACT Neon tetras (Paracheirodon spp.) are three colorful characid species with a complicated taxonomic history, and relationships among the species are poorly known. Molecular data resolved the relationships among the three neon tetras, and strongly supported monophyly of the genus and its sister taxon relationship to Brittanichthys. Additionally, the sister-taxon relationship of the rummy-nose tetras Hemigrammus bleheri and Petitella georgiae was strongly supported by molecular and morphological data. Therefore, we propose to transfer the rummy-nose tetras H. bleheri and H. rhodostomus to the genus Petitella. Furthermore, Petitella georgiae is likely to be a species complex comprised of at least two species.
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Frazão L, Oliveira ME, Menin M, Campos J, Almeida A, Kaefer IL, Hrbek T. Species richness and composition of snake assemblages in poorly accessible areas in the Brazilian Amazonia. Biota Neotrop 2020. [DOI: 10.1590/1676-0611-bn-2018-0661] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract: Snakes are a diverse group of terrestrial vertebrates of the order Squamata. Despite that, in the Amazonian biome, information about distribution and identification of snakes is limited when compared to other groups. Additionally, in Amazonia there is a sampling bias towards areas geographically close to urban centers and more densely populated areas. This in turn leads to false distribution gaps in poorly accessible areas of Amazonia. In this article we report the composition of snake assemblages in six areas of the Brazilian Amazonia, based on field sampling conducted over four years using standardized methods. We sampled 70 species from eight families: Typhlopidae (n=1), Leptotyphlopidae (n=1), Anillidae (n=1), Boidae (n=5), Colubridae (n=15), Dipsadidae (n=35), Elapidae (n=7), and Viperidae (n=5). The largest number of species was recorded in the Trombetas River area and the lowest in the Jatapu River area. The total beta diversity was 0.40 and the snake assemblages were structured mainly by replacement (72.5%). The time-limited search was the method that recorded the greatest number of individuals in the studied areas (44.1%) and also the greatest number of species (n=40). However, some species were recorded only by other methods such as interception by pitfall traps with directional fences. Despite the large number of species sampled in the study, no particular area comprised more than 40% of species registered in all the areas, indicating that snakes are poorly detected even with large sampling effort across multiple areas of a species distribution.
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Affiliation(s)
- Luciana Frazão
- Bionorte - Rede de Biodiversidade e Biotecnologia da Amazônia Legal, Brasil; Universidade Federal do Amazonas, Brasil
| | | | - Marcelo Menin
- Universidade Federal do Amazonas, Brasil; Universidade Federal do Amazonas, Brasil
| | | | - Alexandre Almeida
- Universidade Federal do Amazonas, Brasil; Universidade Federal do Amazonas, Brasil
| | - Igor L. Kaefer
- Universidade Federal do Amazonas, Brasil; Universidade Federal do Amazonas, Brasil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Brasil; Universidade Federal do Amazonas, Brasil
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Ota RP, Machado VN, Andrade MC, Collins RA, Farias IP, Hrbek T. Integrative taxonomy reveals a new species of pacu (Characiformes: Serrasalmidae: Myloplus) from the Brazilian Amazon. Neotrop ichthyol 2020. [DOI: 10.1590/1982-0224-20190112] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
ABSTRACT Pacus of the genus Myloplus represent a formidable taxonomic challenge, and particularly so for the case of M. asterias and M. rubripinnis, two widespread and common species that harbor considerable morphological diversity. Here we apply DNA barcoding and multiple species discovery methods to find candidate species in this complex group. We report on one well-supported lineage that is also morphologically and ecologically distinct. This lineage represents a new species that can be distinguished from congeners by the presence of dark chromatophores on lateral-line scales, which gives the appearance of a black lateral line. It can be further diagnosed by having 25-29 branched dorsal-fin rays (vs. 18-24), 89-114 perforated scales from the supracleithrum to the end of hypural plate (vs. 56-89), and 98-120 total lateral line scales (vs. 59-97). The new species is widely distributed in the Amazon basin, but seems to have a preference for black- and clearwater habitats. This ecological preference and black lateral line color pattern bears a striking similarity to the recently described silver dollar Metynnis melanogrammus.
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Farias IP, Willis S, Leão A, Verba JT, Crossa M, Foresti F, Porto-Foresti F, Sampaio I, Hrbek T. The largest fish in the world's biggest river: Genetic connectivity and conservation of Arapaima gigas in the Amazon and Araguaia-Tocantins drainages. PLoS One 2019; 14:e0220882. [PMID: 31419237 PMCID: PMC6697350 DOI: 10.1371/journal.pone.0220882] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 07/25/2019] [Indexed: 12/02/2022] Open
Abstract
Arapaima, pirarucu or paiche (Arapaima gigas) is one of the largest freshwater fish in the world, and has a long history of commercial exploitation in the Amazon region. To estimate levels of genetic variability and historical and recent connectivity in Arapaima, we examined variation in eleven microsatellite DNA markers in individuals from 22 localities in Brazil, Colombia, and Peru. The results of analysis of molecular variance, Bayesian clustering and discriminant analysis of principal components showed that Arapaima in our samples represents two major populations, one in the Amazonas and one in the Araguaia-Tocantins River basins. The Amazonas population is further structured by isolation-by-distance with the hydrologically largely unconnected Amapá locality representing the eastern-most extreme of this continuum; gene flow predominates at distances of less than 1500 km with localities separated by over 2000 km dominated by genetic drift and effectively forming different populations. We saw no evidence of multiple species of Arapaima in the Amazonas basin, and analysis of pairwise genetic divergence (FST) with Mantel tests and correlograms indicated that this largest population exhibits a large-scale pattern of isolation-by-distance, with which results from MIGRATE-N agreed. The degree and significance of genetic divergence indicates that most sampled localities represent demographically independent sub-populations, although we did identify several recent migration events between both proximal and more distant localities. The levels of genetic diversity were heterogeneous across sites, including low genetic diversity, effective population sizes, and evidence of genetic bottlenecks in several places. On average the levels of gene diversity and rarefied allelic richness were higher for localities along the Amazonas mainstem than in the tributaries, despite these being the areas of highest fishing pressure, while the lowest values were found in tributary headwaters, where landscape modification is a significant threat. We recommend that managers consider the regional and local threats to these populations and tailor strategies accordingly, strategies which should ensure the ability of young A. gigas to disperse through floodplain corridors to maintain genetic diversity among otherwise sedentary adult sub-populations.
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Affiliation(s)
- Izeni Pires Farias
- Laboratório de Evolução e Genética Animal/LEGAL, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
- * E-mail: (IPF); (TH)
| | - Stuart Willis
- Department of Ichthyology, California Academy of Sciences, San Francisco, CA, United States of America
| | - Adam Leão
- Laboratório de Evolução e Genética Animal/LEGAL, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
| | - Júlia Tovar Verba
- Laboratório de Evolução e Genética Animal/LEGAL, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte (UFRN), Natal, Brazil
| | | | - Fausto Foresti
- Laboratório de Biologia e Genética de Peixes, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, São Paulo, Brazil
| | - Fabio Porto-Foresti
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista (UNESP), Campus de Bauru, Bauru, Brazil
| | - Iracilda Sampaio
- Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Universitário de Bragança, Pará, Brazil
| | - Tomas Hrbek
- Laboratório de Evolução e Genética Animal/LEGAL, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
- * E-mail: (IPF); (TH)
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Escobar L MD, Ota RP, Machado-Allison A, Andrade-López J, Farias IP, Hrbek T. A new species of Piaractus (Characiformes: Serrasalmidae) from the Orinoco Basin with a redescription of Piaractus brachypomus. J Fish Biol 2019; 95:411-427. [PMID: 31017302 DOI: 10.1111/jfb.13990] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 04/23/2019] [Indexed: 06/09/2023]
Abstract
Piaractus orinoquensis, a new species of serrasalmid fish, is described from the Orinoco River basin. The new species differs from congeners by having a slenderer body, relatively smaller head and snout, more compressed mid-body, fewer scales above and below the lateral line and diagnostic molecular characters in the coI mitochondrial gene region. We also provide a re-description of Piaractus brachypomus, restricting its geographic distribution to the Amazon River basin. Both species are economically important in their respective basins and need to be independently managed as distinct species.
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Affiliation(s)
- Maria D Escobar L
- Departamento de Genética, Instituto de Ciências Biológicas, Laboratório de Evolução e Genética Animal, Universidade Federal do Amazonas, Manaus, Brazil
- Programa de Pós-Graduação em Ciências Pesqueiras nos Trópicos, Universidade Federal do Amazonas, Manaus, Brazil
| | - Rafaela P Ota
- Instituto Nacional de Pesquisas da Amazônia, Programa de Pós-Graduação em Biologia de Água Doce e Pesca Interior, Manaus, Brazil
| | - Antonio Machado-Allison
- Departamento de Biología, Instituto de Zoología Tropical, Laboratório de Sistemática de Peces, Universidad Central de Venezuela, Caracas, Venezuela
- College of the Environment, Wesleyan University, Middletown, Connecticut, USA
| | - Juana Andrade-López
- Departamento de Biología, Instituto de Zoología Tropical, Laboratório de Sistemática de Peces, Universidad Central de Venezuela, Caracas, Venezuela
| | - Izeni P Farias
- Departamento de Genética, Instituto de Ciências Biológicas, Laboratório de Evolução e Genética Animal, Universidade Federal do Amazonas, Manaus, Brazil
| | - Tomas Hrbek
- Departamento de Genética, Instituto de Ciências Biológicas, Laboratório de Evolução e Genética Animal, Universidade Federal do Amazonas, Manaus, Brazil
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Costa-Araújo R, de Melo FR, Canale GR, Hernández-Rangel SM, Messias MR, Rossi RV, Silva FE, da Silva MNF, Nash SD, Boubli JP, Farias IP, Hrbek T. The Munduruku marmoset: a new monkey species from southern Amazonia. PeerJ 2019; 7:e7019. [PMID: 31380146 PMCID: PMC6661146 DOI: 10.7717/peerj.7019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 04/25/2019] [Indexed: 11/22/2022] Open
Abstract
Although the Atlantic Forest marmosets (Callithrix spp.) are among the best studied Neotropical primates, the Amazonian marmosets (Callibella humilis, Cebuella spp. and Mico spp.) are much less well-known. Even species diversity and distributions are yet to be properly determined because field data and materials currently available in scientific collections do not allow comprehensive taxonomic studies of Amazonian marmosets. From 2015 to 2018, we conducted 10 expeditions in key-areas within southern Amazonia where little or no information on marmosets was available. In one such region-the Tapajós-Jamanxim interfluve-we recorded marmosets with a distinctive pelage pigmentation pattern suggesting they could represent a new species. We tested this hypothesis using an integrative taxonomic framework that included phylogenomic data (ddRAD sequences), pelage pigmentation characters, and distribution records. We found that the marmosets of the northern Tapajós-Jamanxim interfluve have unique states in pelage pigmentation characters, form a clade (100% support) in our Bayesian and Maximum-Likelihood phylogenies, and occur in an area isolated from other taxa by rivers. The integration of these lines of evidence leads us to describe a new marmoset species in the genus Mico, named after the Munduruku Amerindians of the Tapajós-Jamanxim interfluve, southwest of Pará State, Brazil.
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Affiliation(s)
- Rodrigo Costa-Araújo
- Pós-graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brasil
- Departamento de Genética, Universidade Federal do Amazonas, Manaus, Amazonas, Brasil
| | - Fabiano R. de Melo
- Departamento de Engenharia Florestal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brasil
- Unidade Acadêmica Especial Ciências Biológicas, Universidade Federal de Goiás, Jataí, Goiás, Brasil
| | | | | | | | - Rogério Vieira Rossi
- Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brasil
| | - Felipe E. Silva
- School of Environment and Life Sciences, University of Salford, Salford, Manchester, UK
- Ecovert, Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas, Brasil
| | | | - Stephen D. Nash
- Department of Anatomical Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Jean P. Boubli
- School of Environment and Life Sciences, University of Salford, Salford, Manchester, UK
| | - Izeni Pires Farias
- Departamento de Genética, Universidade Federal do Amazonas, Manaus, Amazonas, Brasil
| | - Tomas Hrbek
- Departamento de Genética, Universidade Federal do Amazonas, Manaus, Amazonas, Brasil
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Gravena W, Hrbek T, da Silva VMF, Farias IP. Boto ( Inia geoffrensis-Cetacea: Iniidae) aggregations in two provisioning sites in the lower Negro River-Amazonas, Brazil: are they related? PeerJ 2019; 7:e6692. [PMID: 31024759 PMCID: PMC6475133 DOI: 10.7717/peerj.6692] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 02/28/2019] [Indexed: 11/20/2022] Open
Abstract
The Negro River currently has seven floating houses where tourists can feed and interact with botos, each with its own history of how these aggregations were formed. Some keepers say these groups are familial, even reporting individuals being born into the group. However, behavioral studies have shown that botos are solitary, only forming groups at feeding areas and during the mating season. In the present study we used 12 microsatellite and molecular sex markers to characterize relationships within and between two boto aggregations (ten and seven botos each) in the lower Negro River. Molecular sexing revealed that all botos sampled from both aggregations were males. This may be explained by habitat preference, as male botos are primarily found in the main channels of large rivers, whereas females prefer more protected areas, such as flooded forests and its channels and lakes. Most of the animals were unrelated within each aggregation, demonstrating that these aggregations are not normally formed due to kinship bonds, but are exclusively for feeding, as botos learn that these places provide easy access to food. This study provides important information that helps us understand how human interaction is affecting the social structure and behavior of these animals.
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Affiliation(s)
- Waleska Gravena
- Instituto de Saúde e Biotecnologia (ISB), Universidade Federal do Amazonas (UFAM), Coari, Amazonas, Brazil
- Laboratório de Evolução e Genética Animal (LEGAL), Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
- Laboratório de Mamíferos Aquáticos (LMA), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Amazonas, Brazil
| | - Tomas Hrbek
- Laboratório de Evolução e Genética Animal (LEGAL), Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
| | - Vera Maria Ferreira da Silva
- Laboratório de Mamíferos Aquáticos (LMA), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Amazonas, Brazil
| | - Izeni Pires Farias
- Laboratório de Evolução e Genética Animal (LEGAL), Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
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Bittencourt PS, Campos Z, Muniz FDL, Marioni B, Souza BC, Da Silveira R, de Thoisy B, Hrbek T, Farias IP. Evidence of cryptic lineages within a small South American crocodilian: the Schneider's dwarf caiman Paleosuchus trigonatus (Alligatoridae: Caimaninae). PeerJ 2019; 7:e6580. [PMID: 30931177 PMCID: PMC6433001 DOI: 10.7717/peerj.6580] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 02/01/2019] [Indexed: 11/25/2022] Open
Abstract
Schneider’s dwarf caiman Paleosuchus trigonatus is one of the smallest living crocodilians. Due to its broad distribution, cryptic behavior, and small home range, the species is well suited for the study of phylogeographic patterns on a continental scale. Additionally, this species is under threat due to habitat loss, trade and harvest, but is considered at low conservation risk by the IUCN. In the present study we test the hypothesis that P. trigonatus is comprised of geographically structured lineages. Phylogenetic reconstructions of the mitochondrial cytochrome b gene and single locus species discovery methods revealed the existence of two well-supported lineages within P. trigonatus—an Amazonian and Guianan lineage. Fossil calibrated divergence of these lineages was estimated to have occurred in the Late Miocene (7.5 Ma). The hypothesis that the Atlantic coast drainages might have been colonized from the southeast or central Amazon is supported by demographic metrics and relatively low genetic diversity of the Coastal and upper Branco populations when compared to the Amazon basin populations. The Amazon basin lineage is structured along an east-west gradient, with a sharp transition in haplotype frequencies to the east and west of the Negro and Madeira rivers. These lineages are already under anthropogenic threat and, therefore, are conservation dependent. Recognition of these lineages will foster discussion of conservation future of P. trigonatus and these lineages.
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Affiliation(s)
- Pedro Senna Bittencourt
- Laboratory of Animal Genetics and Evolution (LEGAL), Federal University of Amazonas, Manaus, Amazonas, Brazil.,Graduate Program in Genetics, Conservation, and Evolutionary Biology, National Institute of Amazonian Research (INPA), Manaus, Amazonas, Brazil
| | - Zilca Campos
- Wildlife Laboratory, Brazilian Agricultural Research Corporation (EMBRAPA) Pantanal, Corumbá, Mato Grosso do Sul, Brazil
| | - Fábio de Lima Muniz
- Laboratory of Animal Genetics and Evolution (LEGAL), Federal University of Amazonas, Manaus, Amazonas, Brazil.,Graduate Program in Genetics, Conservation, and Evolutionary Biology, National Institute of Amazonian Research (INPA), Manaus, Amazonas, Brazil
| | - Boris Marioni
- Graduate Program in Freshwater Biology and Inland Fisheries, National Institute of Amazonian Research (INPA), Manaus, Amazonas, Brazil
| | - Bruno Campos Souza
- Chico Mendes Institute for Biodiversity Conservation (ICMBio), Boa Vista, Roraima, Brazil
| | - Ronis Da Silveira
- Laboratory of Zoology Applied to Conservation, Federal University of Amazonas (UFAM), Manaus, Amazonas, Brazil
| | - Benoit de Thoisy
- Institut Pasteur de la Guyane, Cayenne, French Guiana.,Association Kwata, Cayenne, French Guiana
| | - Tomas Hrbek
- Laboratory of Animal Genetics and Evolution (LEGAL), Federal University of Amazonas, Manaus, Amazonas, Brazil
| | - Izeni Pires Farias
- Laboratory of Animal Genetics and Evolution (LEGAL), Federal University of Amazonas, Manaus, Amazonas, Brazil
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38
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Muniz FL, Ximenes AM, Bittencourt PS, Hernández-Rangel SM, Campos Z, Hrbek T, Farias IP. Detecting population structure of Paleosuchus trigonatus (Alligatoridae: Caimaninae) through microsatellites markers developed by next generation sequencing. Mol Biol Rep 2019; 46:2473-2484. [DOI: 10.1007/s11033-019-04709-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 02/16/2019] [Indexed: 12/30/2022]
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Abstract
In the age of genome-scale DNA sequencing, choice of molecular marker arguably remains an important decision in planning a phylogenetic study. Using published genomes from 23 primate species, we make a standardized comparison of four of the most frequently used protocols in phylogenomics, viz., targeted sequence-enrichment using ultraconserved element and exon-capture probes, and restriction-site-associated DNA sequencing (RADseq and ddRADseq). Here, we present a procedure to perform in silico extractions from genomes and create directly comparable data sets for each class of marker. We then compare these data sets in terms of both phylogenetic resolution and ability to consistently and precisely estimate clade ages using fossil-calibrated molecular-clock models. Furthermore, we were also able to directly compare these results to previously published data sets from Sanger-sequenced nuclear exons and mitochondrial genomes under the same analytical conditions. Our results show-although with the exception of the mitochondrial genome data set and the smallest ddRADseq data set-that for uncontroversial nodes all data classes performed equally well, that is they recovered the same well supported topology. However, for one difficult-to-resolve node comprising a rapid diversification, we report well supported but conflicting topologies among the marker classes consistent with the mismodeling of gene tree heterogeneity as demonstrated by species tree analyses of single nucleotide polymorphisms. Likewise, clade age estimates showed consistent discrepancies between data sets under strict and relaxed clock models; for recent nodes, clade ages estimated by nuclear exon data sets were younger than those of the UCE, RADseq and mitochondrial data, but vice versa for the deepest nodes in the primate phylogeny. This observation is explained by temporal differences in phylogenetic informativeness (PI), with the data sets with strong PI peaks toward the present underestimating the deepest node ages. Finally, we conclude by emphasizing that while huge numbers of loci are probably not required for uncontroversial phylogenetic questions-for which practical considerations such as ease of data generation, sharing, and aggregating, therefore become increasingly important-accurately modeling heterogeneous data remains as relevant as ever for the more recalcitrant problems.
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Affiliation(s)
- Rupert A Collins
- Laboratório de Evolução e Genética Animal, Department of Genetics, Federal University of Amazonas, Av. Rodrigo Otavio Ramos, 3000, Manaus, AM, 69077-000, Brazil.,School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Ave, Bristol BS8 1TH, UK
| | - Tomas Hrbek
- Laboratório de Evolução e Genética Animal, Department of Genetics, Federal University of Amazonas, Av. Rodrigo Otavio Ramos, 3000, Manaus, AM, 69077-000, Brazil.,Department of Biology, 4102 LSB Brigham Young University, Provo, UT, 84602, USA
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40
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Rojas RR, Fouquet A, De Carvalho VT, Ron S, Chaparro JC, Vogt RC, Ávila RW, Farias IP, Gordo M, Hrbek T. Redescription of the Amazonian tiny tree toad Amazophrynella minuta (Melin, 1941) (Anura: Bufonidae) from its type locality. Zootaxa 2018; 4482:511-526. [PMID: 30313811 DOI: 10.11646/zootaxa.4482.3.4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Indexed: 11/04/2022]
Abstract
The description of Amazophrynella minuta was published in 1941 by the Swedish naturalist Douglas Melin based on material from Taracuá (Amazonas state, Brazil). This description was very brief and based on the morphology of few specimens with diagnostic characters and color variation not well defined. Moreover, the type series is currently in poor state of conservation. Consequently, taxonomic ambiguity surrounds the nominal taxon A. minuta, which hampers the description of many unnamed congeneric species. Herein, we redescribe A. minuta based on recently collected specimens from the type locality, designate a lectotype, formulate a new diagnosis, provide patterns of morphological variation, measurements and body proportions.
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Affiliation(s)
- Rommel R Rojas
- Laboratório de Evolução e Genética Animal (LEGAL), Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Av. General Rodrigo Octávio Jordão Ramos, 6200. CEP 69077-000 Manaus, AM, Brazil.
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41
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Hrbek T, Meliciano NV, Zuanon J, Farias IP. Remarkable Geographic Structuring of Rheophilic Fishes of the Lower Araguaia River. Front Genet 2018; 9:295. [PMID: 30154824 PMCID: PMC6102472 DOI: 10.3389/fgene.2018.00295] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 07/13/2018] [Indexed: 11/13/2022] Open
Abstract
Rapids and waterfalls, and their associated fauna and flora are in peril. With the construction of each new hydroelectric dam, more rapids and waterfalls are destroyed, leading to the disappearance of associated fauna and flora. Areas of rapids harbor distinct, highly endemic rheophilic fauna and flora adapted to an extreme environment. Rheophilic habitats also have disjunct distribution both within and across rivers. Rheophilic habitats thus represent islands of suitable habitat separated by stretches of unsuitable habitat. In this study, we investigated to what extent, if any, species of cichlid and anostomid fishes associated with rheophilic habitats were structured among the rapids of Araguaia River in the Brazilian Amazon. We tested both for population structuring as well as non-random distribution of lineages among rapids. Eight of the nine species had multiple lineages, five of these nine species were structured, and three of the eight species with multiple lineages showed non-random distribution of lineages among rapids. These results demonstrate that in addition to high levels of endemicism of rheophilic fishes, different rapids even within the same river are occupied by different lineages. Rheophilic species and communities occupying different rapids are, therefore, not interchangeable, and this realization must be taken into account when proposing mitigatory/compensatory measures in hydroelectric projects, and in conservation planning.
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Affiliation(s)
- Tomas Hrbek
- Laboratório de Evolução e Genética Animal, Departmento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Brazil
| | - Natasha V. Meliciano
- Laboratório de Evolução e Genética Animal, Departmento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Brazil
- Instituto de Saúde e Biotecnologia, Universidade Federal do Amazonas, Coari, Brazil
| | - Jansen Zuanon
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Izeni P. Farias
- Laboratório de Evolução e Genética Animal, Departmento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Brazil
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42
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Rojas RR, De Carvalho VT, Ávila RW, Kawashita-Ribeiro RA, Hrbek T, Gordo M. Description of the advertisement calls of four species of Amazophrynella (Anura:Bufonidae). Zootaxa 2018; 4459:193-196. [PMID: 30314140 DOI: 10.11646/zootaxa.4459.1.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Indexed: 11/04/2022]
Abstract
Amazophrynella comprises 11 small bufonid species with a pan-Amazonian distribution (Fouquet et al. 2012a, b; Rojas et al. 2016, Rojas et al. 2018). All species inhabit the forest leaf litter, breed in seasonal puddles and are diurnally and nocturnally active (Fouquet et al. 2012b; Rojas et al. 2014; 2015; 2016). Until now only one nominal species, A. javierbustamantei, and two putative lineages-A. moisesii (Rio Yuyapichis, Peru) and A. siona (Santa Cecilia, Ecuador)-had their advertisement calls formally described (Duellman 1978; Schlüter 1981; Rojas et al. 2016). Herein, we described for the first time the advertisement calls from additional four species of Amazophrynella.
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Affiliation(s)
- Rommel R Rojas
- Laboratório de Genética e Evolução Animal, Departamento de Genética, ICB, Universidade Federal do Amazonas, Av. Gen. Rodrigo Octávio Jordão Ramos, 6200, CEP 69077-000, Manaus, AM, Brazil.
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43
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Santos MDCF, Hrbek T, Farias IP. A Multilocus Approach to Understanding Historical and Contemporary Demography of the Keystone Floodplain Species Colossoma macropomum (Teleostei: Characiformes). Front Genet 2018; 9:263. [PMID: 30154822 PMCID: PMC6102471 DOI: 10.3389/fgene.2018.00263] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 06/28/2018] [Indexed: 11/19/2022] Open
Abstract
We studied the natural populations of a flagship fish species of the Amazon, Colossoma macropomum which in recent years has been suffering from severe exploitation. Our aim was to investigate the existence or not of genetic differentiation across the wide area of its distribution and to investigate changes in its effective population size throughout its evolutionary history. We sampled individuals from 21 locations distributed throughout the Amazon basin. We analyzed 539 individuals for mitochondrial genes (control region and ATPase gene 6/8), generating 1,561 base pairs, and genotyped 604 individuals for 13 microsatellite loci obtaining, on average, 21.4 alleles per locus. Mean HE was 0.78 suggesting moderate levels of genetic variability. AMOVA and other tests used to detect the population structure based on both markers indicate that C. macropomum comprises a single and large panmitic population in the main channel of the Solimões-Amazonas River basin, on the other hand localities in the headwaters of the tributaries Juruá, Purus, Madeira, Tapajós, and localities of black water, showed genetic structure. The greatest genetic differentiation was observed between the Brazilian Amazon basin and the Bolivian sub-basin with restricted genetic flow between the two basins. Demographic analyzes of mitochondrial genes indicated population expansion in the Brazilian and Bolivian Amazon basins during the Pleistocene, and microsatellite data indicated a population reduction during the Holocene. This shows that the historical demography of C. macropomum is highly dynamic. Conservation and management strategies should be designed to respect the existing population structure and minimize the effects of overfishing by limiting fisheries C. macropomum populations.
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Affiliation(s)
| | - Tomas Hrbek
- Laboratório de Evolução e Genética Animal, Departamento de Genética, Universidade Federal do Amazonas, Manaus, Brazil
| | - Izeni P Farias
- Laboratório de Evolução e Genética Animal, Departamento de Genética, Universidade Federal do Amazonas, Manaus, Brazil
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44
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Byrne H, Lynch Alfaro JW, Sampaio I, Farias I, Schneider H, Hrbek T, Boubli JP. Titi monkey biogeography: Parallel Pleistocene spread byPlecturocebusandCheracebusinto a post-Pebas Western Amazon. ZOOL SCR 2018. [DOI: 10.1111/zsc.12300] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Hazel Byrne
- Institute for Society and Genetics; University of California Los Angeles (UCLA); Los Angeles California
| | - Jessica W. Lynch Alfaro
- Institute for Society and Genetics; University of California Los Angeles (UCLA); Los Angeles California
- Department of Anthropology; University of California Los Angeles (UCLA); Los Angeles California
| | - Iracilda Sampaio
- Laboratório de Genética e Biologia Molecular; Universidade Federal do Pará; Bragança Pará Brazil
| | - Izeni Farias
- Laboratório de Evolução e Genética Animal; Universidade Federal do Amazonas; Manaus Amazonas Brazil
| | - Horacio Schneider
- Laboratório de Genética e Biologia Molecular; Universidade Federal do Pará; Bragança Pará Brazil
| | - Tomas Hrbek
- Laboratório de Evolução e Genética Animal; Universidade Federal do Amazonas; Manaus Amazonas Brazil
| | - Jean P. Boubli
- School of Environment and Life Sciences; University of Salford; Salford UK
- Programa de Pos-graduação em Genética, Conservaçāo e Evolução; Instituto Nacional de Pesquisas da Amazônia; Manaus Amazonas Brazil
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45
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Rojas RR, Fouquet A, Ron SR, Hernández-Ruz EJ, Melo-Sampaio PR, Chaparro JC, Vogt RC, de Carvalho VT, Pinheiro LC, Avila RW, Farias IP, Gordo M, Hrbek T. A Pan-Amazonian species delimitation: high species diversity within the genus Amazophrynella (Anura: Bufonidae). PeerJ 2018; 6:e4941. [PMID: 30013824 PMCID: PMC6042491 DOI: 10.7717/peerj.4941] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/21/2018] [Indexed: 11/20/2022] Open
Abstract
Amphibians are probably the most vulnerable group to climate change and climate-change associate diseases. This ongoing biodiversity crisis makes it thus imperative to improve the taxonomy of anurans in biodiverse but understudied areas such as Amazonia. In this study, we applied robust integrative taxonomic methods combining genetic (mitochondrial 16S, 12S and COI genes), morphological and environmental data to delimit species of the genus Amazophrynella (Anura: Bufonidae) sampled from throughout their pan-Amazonian distribution. Our study confirms the hypothesis that the species diversity of the genus is grossly underestimated. Our analyses suggest the existence of eighteen linages of which seven are nominal species, three Deep Conspecific Lineages, one Unconfirmed Candidate Species, three Uncategorized Lineages, and four Confirmed Candidate Species and described herein. We also propose a phylogenetic hypothesis for the genus and discuss its implications for historical biogeography of this Amazonian group.
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Affiliation(s)
- Rommel R Rojas
- Laboratory of Evolution and Animal Genetics, Department of Genetics, ICB, Universidade Federal do Amazonas, Brazil
| | - Antoine Fouquet
- Laboratoire Ecologie, Evolution et Interactions des Systèmes Amazoniens, Centre de recherche de Montabo, Cayenne, French Guiana
| | - Santiago R Ron
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Emil José Hernández-Ruz
- Laboratório de Zoologia, Faculdade de Ciências Biológicas, Campus Universitário de Altamira, Universidade Federal do Pará, Altamira, Para, Brazil
| | - Paulo R Melo-Sampaio
- Departamento de Vertebrados, Museu Nacional, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Juan C Chaparro
- Coleccion de anfibios y reptiles, Museo de la Biodiversidad, Cusco, Peru.,Museo de Historia Natural, Universidad Nacional de San Antonio Abad, Cusco, Peru
| | - Richard C Vogt
- CEQUA, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Vinicius Tadeu de Carvalho
- Laboratory of Evolution and Animal Genetics, Department of Genetics, ICB, Universidade Federal do Amazonas, Brazil.,Departamento de Ciências Biológicas, Centro de Ciências Biológicas e da Saúde, Universidade Regional do Cariri, Crato, Ceara, Brazil
| | | | - Robson W Avila
- Departamento de Ciências Biológicas, Centro de Ciências Biológicas e da Saúde, Universidade Regional do Cariri, Crato, Ceara, Brazil
| | - Izeni Pires Farias
- Laboratory of Evolution and Animal Genetics, Department of Genetics, ICB, Universidade Federal do Amazonas, Brazil
| | - Marcelo Gordo
- Departamento de Biologia, ICB, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | - Tomas Hrbek
- Laboratory of Evolution and Animal Genetics, Department of Genetics, ICB, Universidade Federal do Amazonas, Brazil
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Motta J, Menin M, Almeida AP, Hrbek T, Farias IP. When the unknown lives next door: a study of central Amazonian anurofauna. Zootaxa 2018; 4438:79-104. [PMID: 30313157 DOI: 10.11646/zootaxa.4438.1.3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Indexed: 11/04/2022]
Abstract
The number of species of anurans in the Amazon is highly underestimated with new studies reporting the discovery of a large number of species every year. This advance in the discovery of biodiversity is due to the use of molecular tools, especially 16S rRNA gene barcoding, which is used to identify species and discover cryptic lineages. Few anurans of the central Amazon have molecular sequence data available in public databases, which contrasts with the considerable species richness of this biome. The aim of the present study was to test for the presence of cryptic species using the mPTP delimitation algorism. We morphologically identified 26 species, of which 23 were confirmed molecularly with the remaining three species identified as other congeneric species, since sequences with the same epithet do not exist in GenBank. Of these 23 species, nine contained one lineage restricted to central Amazon. This represents an underestimate of 39% in the taxonomic diversity in our sample. This is particularly surprising given that our sampling sites are among the best-studied regions of the central Amazon.
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Affiliation(s)
- Jessica Motta
- Laboratório de Evolução e Genética Animal (LEGAL), Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Av. General Rodrigo Otávio Jordão Ramos, 6200, 69077-000 Manaus, AM, Brazi.
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Machado VN, Collins RA, Ota RP, Andrade MC, Farias IP, Hrbek T. One thousand DNA barcodes of piranhas and pacus reveal geographic structure and unrecognised diversity in the Amazon. Sci Rep 2018; 8:8387. [PMID: 29849152 PMCID: PMC5976771 DOI: 10.1038/s41598-018-26550-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 05/10/2018] [Indexed: 11/25/2022] Open
Abstract
Piranhas and pacus (Characiformes: Serrasalmidae) are a charismatic but understudied family of Neotropical fishes. Here, we analyse a DNA barcode dataset comprising 1,122 specimens, 69 species, 16 genera, 208 localities, and 34 major river drainages in order to make an inventory of diversity and to highlight taxa and biogeographic areas worthy of further sampling effort and conservation protection. Using four methods of species discovery-incorporating both tree and distance based techniques-we report between 76 and 99 species-like clusters, i.e. between 20% and 33% of a priori identified taxonomic species were represented by more than one mtDNA lineage. There was a high degree of congruence between clusters, with 60% supported by three or four methods. Pacus of the genus Myloplus exhibited the most intraspecific variation, with six of the 13 species sampled found to have multiple lineages. Conversely, piranhas of the Serrasalmus rhombeus group proved difficult to delimit with these methods due to genetic similarity and polyphyly. Overall, our results recognise substantially underestimated diversity in the serrasalmids, and emphasise the Guiana and Brazilian Shield rivers as biogeographically important areas with multiple cases of across-shield and within-shield diversifications. We additionally highlight the distinctiveness and complex phylogeographic history of rheophilic taxa in particular, and suggest multiple colonisations of these habitats by different serrasalmid lineages.
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Affiliation(s)
- Valeria N Machado
- Laboratório de Evolução e Genétic Animal, Departamento de Genética, Universidade Federal do Amazonas, Av., General Rodrigo Otávio Jordão, 3000, 69077-000, Manaus, AM, Brazil
| | - Rupert A Collins
- Laboratório de Evolução e Genétic Animal, Departamento de Genética, Universidade Federal do Amazonas, Av., General Rodrigo Otávio Jordão, 3000, 69077-000, Manaus, AM, Brazil.
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK.
| | - Rafaela P Ota
- Programa de Pós-Graduação em Biologia de Água Doce e Pesca Interior, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936, CP 2223, Petrópolis, 69080-971, Manaus, AM, Brazil
| | - Marcelo C Andrade
- Programa de Pós-Graduação em Ecologia Aquática e Pesca, Instituto de Ciências Biológicas, Universidade Federal do Pará, Av. Perimetral, 2651, Terra Firme, 66040-830, Belém, PA, Brazil
| | - Izeni P Farias
- Laboratório de Evolução e Genétic Animal, Departamento de Genética, Universidade Federal do Amazonas, Av., General Rodrigo Otávio Jordão, 3000, 69077-000, Manaus, AM, Brazil
| | - Tomas Hrbek
- Laboratório de Evolução e Genétic Animal, Departamento de Genética, Universidade Federal do Amazonas, Av., General Rodrigo Otávio Jordão, 3000, 69077-000, Manaus, AM, Brazil.
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Collins RA, Bifi AG, de Oliveira RR, Ribeiro ED, Lujan NK, Rapp Py-Daniel LH, Hrbek T. Biogeography and species delimitation of the rheophilic suckermouth catfish genus Pseudolithoxus (Siluriformes: Loricariidae), with the description of a new species from the Brazilian Amazon. SYST BIODIVERS 2018. [DOI: 10.1080/14772000.2018.1468362] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Rupert A. Collins
- Laboratório de Evolução e Genética Animal, Departamento de Biologia, Universidade Federal do Amazonas, Manaus, AM, Brazil
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Alessandro G. Bifi
- Coordenação em Biodiversidade, Coleção de Peixes, Programa de Coleções Científicas Biológicas-PCCB, Instituto Nacional de Pesquisas da Amazônia-INPA, Av. Andre Araújo 2936, Petrópolis, CEP 69067-375 Manaus, AM, Brazil
| | - Renildo R. de Oliveira
- Coordenação em Biodiversidade, Coleção de Peixes, Programa de Coleções Científicas Biológicas-PCCB, Instituto Nacional de Pesquisas da Amazônia-INPA, Av. Andre Araújo 2936, Petrópolis, CEP 69067-375 Manaus, AM, Brazil
| | - Emanuell D. Ribeiro
- Laboratório de Evolução e Genética Animal, Departamento de Biologia, Universidade Federal do Amazonas, Manaus, AM, Brazil
- Department of Biology, University of Puerto Rico – Río Piedras, PO Box 23360, San Juan, Puerto Rico
| | - Nathan K. Lujan
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, M1C 1A4, Canada
| | - Lúcia H. Rapp Py-Daniel
- Coordenação em Biodiversidade, Coleção de Peixes, Programa de Coleções Científicas Biológicas-PCCB, Instituto Nacional de Pesquisas da Amazônia-INPA, Av. Andre Araújo 2936, Petrópolis, CEP 69067-375 Manaus, AM, Brazil
| | - Tomas Hrbek
- Laboratório de Evolução e Genética Animal, Departamento de Biologia, Universidade Federal do Amazonas, Manaus, AM, Brazil
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Carneiro J, Sampaio I, de Sousa E Silva-Júnior J, Farias I, Hrbek T, Pissinatti A, Silva R, Martins-Junior A, Boubli J, Ferrari SF, Schneider H. Phylogeny, molecular dating and zoogeographic history of the titi monkeys (Callicebus, Pitheciidae) of eastern Brazil. Mol Phylogenet Evol 2018; 124:10-15. [PMID: 29505826 DOI: 10.1016/j.ympev.2018.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 11/23/2017] [Accepted: 03/01/2018] [Indexed: 10/17/2022]
Abstract
The titi monkeys belong to a genus of New World primates endemic to South America, which were recently reclassified in three genera (Cheracebus, Plecturocebus and Callicebus). The genus Callicebus, which currently includes five species, is endemic to eastern Brazil, occurring in the Caatinga, Savanna, and Atlantic Forest biomes. In the present study, we investigated the validity of these species and inferred their phylogenetic relationships, divergence times, and biogeographic patterns based on the molecular analysis of a concatenated sequence of 11 mitochondrial and nuclear DNA markers, derived from 13 specimens. We ran Maximum Likelihood (ML) and Bayesian Inference (BI) analyses, and estimated genetic distances, divergence times. Ancestral areas were estimated on BioGeoBears. Our results suggest that at about twelve million years ago, the ancestor of all titi monkeys inhabited a wide area that extended from the Amazon forest to the South of the Atlantic forest. A first vicariant event originated Cheracebus in the West of the Amazon and the ancestor of Callicebus and Plectorocebus which, later were separated by a second one. The diversification of Callicebus occurred during the Plio-Pleistocene (beginning at 5 Ma) probably influenced by climatic fluctuations and geological events. Therefore, the results of the present work confirmed the existence of five species that currently inhabit forested areas under increasing threat from human activities. Thus, a reliable diagnosis of the taxonomic status of species living in endangered environments is extremely important for the development of conservation measures.
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Affiliation(s)
- Jeferson Carneiro
- Institute of Coastal Studies, Universidade Federal do Pará, Campus Universitário de Bragança, Pará, Brazil.
| | - Iracilda Sampaio
- Institute of Coastal Studies, Universidade Federal do Pará, Campus Universitário de Bragança, Pará, Brazil.
| | | | - Izeni Farias
- Universidade Federal do Amazonas, Manaus, Brazil.
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Manaus, Brazil.
| | | | - Ronylson Silva
- Institute of Coastal Studies, Universidade Federal do Pará, Campus Universitário de Bragança, Pará, Brazil.
| | - Antônio Martins-Junior
- Institute of Coastal Studies, Universidade Federal do Pará, Campus Universitário de Bragança, Pará, Brazil.
| | - Jean Boubli
- School of Environment and Life Sciences, University of Salford, England, United Kingdom.
| | | | - Horacio Schneider
- Institute of Coastal Studies, Universidade Federal do Pará, Campus Universitário de Bragança, Pará, Brazil.
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Boubli JP, da Silva MN, Rylands AB, Nash SD, Bertuol F, Nunes M, Mittermeier RA, Byrne H, Silva FE, Röhe F, Sampaio I, Schneider H, Farias IP, Hrbek T. How many pygmy marmoset (Cebuella Gray, 1870) species are there? A taxonomic re-appraisal based on new molecular evidence. Mol Phylogenet Evol 2018; 120:170-182. [DOI: 10.1016/j.ympev.2017.11.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 10/10/2017] [Accepted: 11/22/2017] [Indexed: 10/18/2022]
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